Hi Justin, your suggestion got close. However, let me give an example. You can use the Gly-Gly-Gly example I am attaching and do this:<div><br></div><div>pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top -water none</div>
<div>/sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr -pp aGGGp.top</div><div><br></div><div>if you look at aGGGp.top I can't find which parameters were used for </div><div><br></div><div><div>[ dihedrals ]</div>
<div>; ai aj ak al funct c0 c1 c2 c3 c4 c5</div><div> 2 1 5 6 9 </div><div><br></div><div>I.e., for proper dihedral (H1- N- CA- HA1), I can't find in amber99sb.ff/forcefield.itp any combination that handles parameters for X-N-CA-X or X-CA-N-X, so how grompp is interpreting this dihedral?</div>
<div><br></div>Thanks,</div><div><br></div><div>Alan</div><div><br><div class="gmail_quote">On 21 May 2012 18:50, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="HOEnZb"><div class="h5"><br>
<br>
On 5/21/12 2:43 PM, Alan wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi there,<br>
<br>
Is there an option in pdb2gmx that when generating the top/itp file, it could<br>
show the parameters explicitly? e.g.:<br>
<br>
Instead of:<br>
[ dihedrals ]<br>
; ai aj ak al funct c0 c1 c2<br>
c3<br>
5 13 11 12 4<br>
11 15 13 14 4<br>
15 23 21 22 4<br>
21 25 23 24 4<br>
25 32 31 33 4<br>
<br>
(my hard hand modifications)<br>
<br>
[ dihedrals ] ; impropers<br>
; treated as propers in GROMACS to use correct AMBER analytical function<br>
; i j k l func phase kd pn<br>
5 13 11 12 4 180.00 43.93200 2 ; CA- N-<br>
C- O<br>
11 15 13 14 4 180.00 4.60240 2 ; C- CA-<br>
N- H<br>
15 23 21 22 4 180.00 43.93200 2 ; CA- N-<br>
C- O<br>
21 25 23 24 4 180.00 4.60240 2 ; C- CA-<br>
N- H<br>
25 32 31 33 4 180.00 43.93200 2 ; CA- OC1-<br>
C- OC2<br>
<br>
I mean, if the parameters that are hiding in e.g. ...gromacs/top/amber99sb.ff<br>
could be showed in the top/itp file for human readers, that would be great.<br>
<br>
</blockquote>
<br></div></div>
You can obtain these parameters (I believe) by running grompp with the -pp option. If you think it would be a useful feature for pdb2gmx, file a feature request on <a href="http://redmine.gromacs.org" target="_blank">redmine.gromacs.org</a>.<br>
<br>
-Justin<span class="HOEnZb"><font color="#888888"><br>
<br>
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Justin A. Lemkul, Ph.D.<br>
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Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>Alan Wilter SOUSA da SILVA, DSc<div>Bioinformatician, UniProt - PANDA, EMBL-EBI<br>CB10 1SD, Hinxton, Cambridge, UK</div><div>+44 1223 49 4588</div>
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