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<div align="center"> <font size="5"> <b><font face="Arial, Helvetica, sans-serif"><a name="top"></a>MCCCS
Towhee (Gromos 43A1)</font></b> </font> </div>
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<td width="697" valign="top"> <b>Overview</b>
<ul>
This section covers the Gromos 43A1 force field as it is implemented into the towhee_ff_Gromos43A1 file in the
ForceFields directory. All of the Towhee atom, bond angle, and dihedral potential numbers for the Gromos 43A1 force
field are listed, along with a short description of their meanings. Unlike almost
all of the other force fields implemented into Towhee, Gromos 43A1 cannot be used with
the molecule assembler (inpstyle 2) as they have not presented their parameters in a way
that facilitates such an assembler, and I have not yet figured out how to create a set of
atom types that would work with the assembler. One of the main barriers to such an assembler
is that Gromos 43A1 does not apply the same torsional potential to all dihedrals that are connected
by the same atom types. Instead Gromos 43A1 applies the torsional potential to only one of the torsions
across the same two central atoms of a dihedral, and the rest interact only via 1-4 van der Waals and
coulombic terms.
For more information about the Gromos force field see the
<a href="http://www.igc.ethz.ch/gromos/">Gromos web site</a>.
Note that Gromos 43A1 is a Lennard-Jones (12-6) force field, but it has a rather complex algorithm for
computing the cross interactions and so its parameters are listed explicitly (starting with Towhee
Version 4.4.0) and so you cannot mix it with any of the other force fields in Towhee.
I would like to acknowledge Lukas D. Schuler for providing very useful
guidance about implementing Gromos 43A1, and a copy of the relevent pages of the Gromos manual.
Any discrepencies (especially typos)
from the published Gromos 43A1 force field values are the sole responsibility
of Marcus G. Martin, and I welcome feedback on how this implementation compares
with other programs.
<p> </p>
</ul>
<b>References for Gromos 43A1</b>
<ul>
The literature reference for Gromos 43A1 is
<ul>
<li><a href="../references.html#scott_et_al_1999">Scott <i>et al.</i> 1999</a></li>
</ul>
Unfortunately this reference does not actually contain the Gromos 43A1 parameters. In order to get the parameters
you need a copy of the Gromos users manual. It appears that the only way to get the users manual is to purchase the
Gromos code, but here is the reference for the users manual in case you want to give it a try.
<ul>
<li><a href="../references.html#van_gunsteren_et_al_1996">van Gunsteren <i>et al.</i> 1996</a></li>
</ul>
A copy of the portions of the users manual related to the force field was generously provided to me by Lukas D. Schuler.
</ul>
<b>Gromos 43A1 Towhee</b>
<ul>
The official force field name for Gromos 43A1 in Towhee is 'Gromos43A1', although that will not get you very far
as the molecule assembler does not yet work for Gromos43A1. In order to make the use of Gromos 43A1 as convienent
as possible without the use of the molecule builder, I have numbered the atoms, vibrations, bending angles, dihedral angles,
and improper torsions using (almost) the same numbering conventions as Gromos 43A1. You will be forced to use inpstyle 0,
but hopefully these lists will make the task possible for those who really wish to use Gromos 43A1. The descriptions below
include the comments from the Gromos users manual, with any additional comments I felt useful in [square brackets].
<dt><font color="red">Atom numbers</font> : <b>Gromos atom name</b> : description of the atom</dt>
<ul>
<li><font color="red">1</font> : <b>O</b> : carbonyl oxygen (C=0)</li>
<li><font color="red">2</font> : <b>OM</b> : carboxyl oxygen (CO)</li>
<li><font color="red">3</font> : <b>OA</b> : hydroxyl, sugar or ester oxygen</li>
<li><font color="red">4</font> : <b>OW</b> : water oxygen</li>
<li><font color="red">5</font> : <b>N</b> : peptide nitrogen (NH)</li>
<li><font color="red">6</font> : <b>NT</b> : terminal nitrogen (NH<sub>2</sub>)</li>
<li><font color="red">7</font> : <b>NL</b> : terminal nitrogen (NH<sub>3</sub>)</li>
<li><font color="red">8</font> : <b>NR</b> : aromatic nitrogen</li>
<li><font color="red">9</font> : <b>NZ</b> : Arg NH (NH<sub>2</sub>)</li>
<li><font color="red">10</font> : <b>NE</b> : Arg NE (NH)</li>
<li><font color="red">11</font> : <b>C</b> : bare carbon</li>
<li><font color="red">12</font> : <b>CH1</b> : aliphatic or sugar CH group</li>
<li><font color="red">13</font> : <b>CH2</b> : aliphatic or sugar CH<sub>2</sub> group</li>
<li><font color="red">14</font> : <b>CH3</b> : aliphatic CH<sub>3</sub> group</li>
<li><font color="red">15</font> : <b>CH4</b> : methane</li>
<li><font color="red">16</font> : <b>CR1</b> : aromatic CH group</li>
<li><font color="red">17</font> : <b>HC</b> : hydrogen bond to carbon [where the carbon is not aliphatic or you would use the
appropriate united-atom CHx group]</li>
<li><font color="red">18</font> : <b>H</b> : hydrogen not bound to carbon</li>
<li><font color="red">19</font> : <b>DUM</b> : dummy atom [not sure what this is for, but implemented it anyway]</li>
<li><font color="red">20</font> : <b>S</b> : sulfur</li>
<li><font color="red">21</font> : <b>CU1+</b> : copper (charge 1+)</li>
<li><font color="red">22</font> : <b>CU2+</b> : copper (charge 2+)</li>
<li><font color="red">23</font> : <b>FE</b> : iron (heme)</li>
<li><font color="red">24</font> : <b>ZN2+</b> : zinc (charge 2+)</li>
<li><font color="red">25</font> : <b>MG2+</b> : magnesium (charge 2+)</li>
<li><font color="red">26</font> : <b>CA2+</b> : calcium (charge 2+)</li>
<li><font color="red">27</font> : <b>P</b> : phosphorous</li>
<li><font color="red">28</font> : <b>AR</b> : argon</li>
<li><font color="red">29</font> : <b>F</b> : fluorine (non-ionic)</li>
<li><font color="red">30</font> : <b>CL</b> : chlorine (non-ionic)</li>
<li><font color="red">31</font> : <b>BR</b> : bromine (non-ionic)</li>
<li><font color="red">32</font> : <b>CMet</b> : CH<sub>3</sub> group in methanol</li>
<li><font color="red">33</font> : <b>OMet</b> : oxygen in methanol</li>
<li><font color="red">34</font> : <b>NA+</b> : sodium (charge 1+)</li>
<li><font color="red">35</font> : <b>CL-</b> : chlorine (charge 1-)</li>
<li><font color="red">36</font> : <b>CChl</b> : carbon in chloroform</li>
<li><font color="red">37</font> : <b>CLChl</b> : chlorine in chloroform</li>
<li><font color="red">38</font> : <b>HChl</b> : hydrogen in chloroform</li>
<li><font color="red">39</font> : <b>SDmso</b> : sulfur in DMSO</li>
<li><font color="red">40</font> : <b>CDmso</b> : CH<sub>3</sub> group in DMSO</li>
<li><font color="red">41</font> : <b>ODmso</b> : oxygen in DMSO</li>
<li><font color="red">42</font> : <b>CCl4</b> : carbon in carbontetrachloride</li>
<li><font color="red">43</font> : <b>CLCl4</b> : chlorine in carbontetrachloride</li>
<li><font color="red">44</font> : <b>SI</b> : silicon</li>
</ul>
<dt><font color="red">Bond Vibration numbers</font> : Gromos examples of the vibration</dt>
<ul>
<li><font color="red">1</font> : H-OA</li>
<li><font color="red">2</font> : H-N (all)</li>
<li><font color="red">3</font> : HC-C</li>
<li><font color="red">4</font> : C-O</li>
<li><font color="red">5</font> : C-OM</li>
<li><font color="red">6</font> : CR1-NR (6-ring)</li>
<li><font color="red">7</font> : H-S</li>
<li><font color="red">8</font> : C-NT,NL</li>
<li><font color="red">9</font> : C,CR1-N,NR,CR1,C (peptide, 5-ring)</li>
<li><font color="red">10</font> : C-N,NA,NE</li>
<li><font color="red">11</font> : C-NR (no H)(6-ring)</li>
<li><font color="red">12</font> : C-OA</li>
<li><font color="red">13</font> : C-NR (heme)</li>
<li><font color="red">14</font> : CH2-C,CR1 (6-ring)</li>
<li><font color="red">15</font> : C,CR1-CH2,C,CR1 (6-ring)</li>
<li><font color="red">16</font> : C,CR1,CH2-NR (6-ring)</li>
<li><font color="red">17</font> : CHn-OA</li>
<li><font color="red">18</font> : CHn-OM</li>
<li><font color="red">19</font> : CHn-OA (sugar)</li>
<li><font color="red">20</font> : CHn-N,NT,NL,NZ,NE</li>
<li><font color="red">21</font> : CHn-NR (5-ring)</li>
<li><font color="red">22</font> : CHn-NR (6-ring)</li>
<li><font color="red">23</font> : O,OM-P</li>
<li><font color="red">24</font> : O-S</li>
<li><font color="red">25</font> : CHn-CHn (sugar)</li>
<li><font color="red">26</font> : C,CHn-C,CHn</li>
<li><font color="red">27</font> : OA-P</li>
<li><font color="red">28</font> : OA-SI</li>
<li><font color="red">29</font> : CH3-S</li>
<li><font color="red">30</font> : CH2-S</li>
<li><font color="red">31</font> : CH1-SI</li>
<li><font color="red">32</font> : NR-FE</li>
<li><font color="red">33</font> : S-S</li>
<li><font color="red">34</font> : NR(heme)-FE</li>
<li><font color="red">35</font> : HWat-OWat</li>
<li><font color="red">36</font> : HChl-CChl</li>
<li><font color="red">37</font> : CChl-CLChl</li>
<li><font color="red">38</font> : ODmso-SDmso</li>
<li><font color="red">39</font> : SDmso-CDmso</li>
<li><font color="red">40</font> : CCl4-CLCl4</li>
<li><font color="red">41</font> : HWat-HWat [I believe this is for use with shake, Towhee cannot handle cyclic 3-mers]</li>
<li><font color="red">42</font> : HChl-CLChl</li>
<li><font color="red">43</font> : CLChl-CLChl</li>
<li><font color="red">44</font> : ODmso-CDmso</li>
<li><font color="red">45</font> : CDmso-CDmso</li>
<li><font color="red">46</font> : HMet-CMet</li>
<li><font color="red">47</font> : CLCl4-CLCl4</li>
</ul>
<dt><font color="red">Bending Angle numbers</font> : Gromos examples of the bending angle</dt>
<ul>
<li><font color="red">1</font> : NR(heme)-FE-NR(heme)</li>
<li><font color="red">2</font> : H-S-CH2</li>
<li><font color="red">3</font> : CH2-S-CH3</li>
<li><font color="red">4</font> : OA-P-OA</li>
<li><font color="red">5</font> : CH2-S-S</li>
<li><font color="red">6</font> : NR-C-CR1 (5-ring)</li>
<li><font color="red">7</font> : CHn-CHn-CHn,NR(6-ring)(sugar)</li>
<li><font color="red">8</font> : CHn,OA-CHn-OA,NR(ring)(sugar)</li>
<li><font color="red">9</font> : H-NL,NT-H ; CHn-OA-CHn(sugar)</li>
<li><font color="red">10</font> : H-NL-C,CHn ; H-NT-CHn</li>
<li><font color="red">11</font> : X-OA,SI-X</li>
<li><font color="red">12</font> : CHn,C-CHn-C,CHn,OA,OM,N,NE</li>
<li><font color="red">13</font> : OM-P-OA</li>
<li><font color="red">14</font> : CHn-CHn-C,CHn,OA,NR,NT,NL</li>
<li><font color="red">15</font> : CHn-CH2-S</li>
<li><font color="red">16</font> : NR(heme)-FE-NR</li>
<li><font color="red">17</font> : H-N-CHn</li>
<li><font color="red">18</font> : CHn,C-C-OA,N,NT,NL</li>
<li><font color="red">19</font> : H-NE-CH2</li>
<li><font color="red">20</font> : CH2-N-CH1</li>
<li><font color="red">21</font> : CH3-N-C ; CHn-C-OM</li>
<li><font color="red">22</font> : H-NT,NZ,NE-C</li>
<li><font color="red">23</font> : H-NT,NZ-H</li>
<li><font color="red">24</font> : H-N-CH3,H,HC (6-ring) ; H-NT-CHn</li>
<li><font color="red">25</font> : P,SI-OA-CHn,P</li>
<li><font color="red">26</font> : N-C-CR1 (6-ring, no H)</li>
<li><font color="red">27</font> : NZ-C-NZ,NE</li>
<li><font color="red">28</font> : OM-P-OM</li>
<li><font color="red">29</font> : O-C-CHn,C ; CH3-N-CHn</li>
<li><font color="red">30</font> : CH1,CH2-N-C</li>
<li><font color="red">31</font> : H-N-C</li>
<li><font color="red">32</font> : O-C-OA,N,NT,NL ; C-NE-CH2</li>
<li><font color="red">33</font> : FE-NR-CR1(5-ring)</li>
<li><font color="red">34</font> : - [no description is listed about this bending angle in Gromos]</li>
<li><font color="red">35</font> : H,HC-5-ring [H atoms bonded to an atom which is part of a 5-ring]</li>
<li><font color="red">36</font> : X(noH)-5-ring [non-H atoms bonded to an atom which is part of a 5-ring]</li>
<li><font color="red">37</font> : OM-C-OM</li>
<li><font color="red">38</font> : 5,6 ring connection</li>
<li><font color="red">39</font> : SI-OA-SI</li>
<li><font color="red">40</font> : HWat-OWat-HWat</li>
<li><font color="red">41</font> : HChl-CChl-CLChl</li>
<li><font color="red">42</font> : CLChl-CChl-CLChl</li>
<li><font color="red">43</font> : CDmso-SDmso-CDmso</li>
<li><font color="red">44</font> : CDmso-SDmso-ODmso</li>
<li><font color="red">45</font> : HMet-OMet-CMet</li>
<li><font color="red">46</font> : CLCl4-CCl4-CLCl4</li>
</ul>
<dt><font color="red">Regular Torsion numbers</font> : Gromos examples of the regular torsion</dt>
<ul>
Note: Gromos 43A1 only applies one torsion involving the cosine series to each pair of central atoms. The remainder of
the torsions only interact via van der Waals and coulombic terms. In Towhee this means you need to set all of the other
torsions to the Null torsion type of 6. I have put an X for any atom.
<li><font color="red">1</font> : X-C-C-X </li>
<li><font color="red">2</font> : X-C-OA-X (at ring)</li>
<li><font color="red">3</font> : X-C-OA-X (carboxyl)</li>
<li><font color="red">4</font> : X-C-N,NT,NE,NZ,NR-X</li>
<li><font color="red">5</font> : X-C-CR1-X (6-ring)</li>
<li><font color="red">6</font> : X-CH1(sugar)-NR(base)-X Also used as the NULL torsion.</li>
<li><font color="red">7</font> : O-CH1-CHn-not O</li>
<li><font color="red">8</font> : O-CH1-CHn-O</li>
<li><font color="red">9</font> : X-OA-P-X</li>
<li><font color="red">10</font> : X-S-S-X</li>
<li><font color="red">11</font> : X-OA-P-X</li>
<li><font color="red">12</font> : X-CHn-OA(not sugar)-X</li>
<li><font color="red">13</font> : X-CH2-S-X</li>
<li><font color="red">14</font> : X-C,CHn,SI-NT,NL,OA(sugar)-X</li>
<li><font color="red">15</font> : HC-C-S-X</li>
<li><font color="red">16</font> : HC-C-C-X</li>
<li><font color="red">17</font> : X-CHn,SI-CHn-X</li>
<li><font color="red">18</font> : X-NR-FE-X</li>
<li><font color="red">19</font> : X-CHn-N,NE-X</li>
<li><font color="red">20</font> : X-CHn-C,NR(ring),CR1-X</li>
<li><font color="red">21</font> : X-CHn-NT-X</li>
</ul>
</ul>
<b>Coulombic interactions</b>
<ul>
Gromos 43A1 uses point charges to represent the molecular electrostatic interactions. There is no automated system for
assigning these charges. Instead, you need to look through the Gromos manual (
<a href="../references.html#van_gunsteren_et_al_1996">van Gunsteren <i>et al.</i> 1996</a>)
and find molecules which are similar to the one you wish to study.
</ul>
<b>Improper torsions</b>
<ul>
Gromos 43A1 exclusively uses the out-of-plane version of the improper torsions. There are only three types of
Gromos 43A1 improper
torsions, one for enforcing tetrahedral conformations, one for enforcing planarity, and a special one for heme.
In the towhee_input file this improper torsion is specified starting from the central atom, and then three atoms
bonded to that
atom are listed. Starting with version 2.4.5, Towhee uses the same numbering convention as Gromos 43A1.
You will need to specify one of the types listed below.
<dt><font color="red">Towhee Improper Torsion number</font> : description</dt>
<ul>
<li><font color="red">1</font> : planar groups </li>
<li><font color="red">2</font> : tetrahedral centers </li>
<li><font color="red">3</font> : heme iron </li>
</ul>
</ul>
<b>Proteins</b>
<ul>
Gromos 43A1 is designed for proteins, but I have not yet implemented this force field into the protein builder.
</ul>
<a href="../towhee_capabilities.html">Return to the Towhee Capabilities web page</a>
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<i><font size="2">Send comments to:</font></i> <font size="2">
<a href="mailto:marcus_martin@users.sourceforge.net">Marcus G. Martin</a><br>
<i>Last updated:</i>
<!-- #BeginDate format:Am1 -->September 07, 2005<!-- #EndDate -->
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