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:
pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top -water none /sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr -pp aGGGp.top if you look at aGGGp.top I can't find which parameters were used for [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 5 6 9 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? Thanks, Alan On 21 May 2012 18:50, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > On 5/21/12 2:43 PM, Alan wrote: > >> Hi there, >> >> Is there an option in pdb2gmx that when generating the top/itp file, it >> could >> show the parameters explicitly? e.g.: >> >> Instead of: >> [ dihedrals ] >> ; ai aj ak al funct c0 c1 c2 >> c3 >> 5 13 11 12 4 >> 11 15 13 14 4 >> 15 23 21 22 4 >> 21 25 23 24 4 >> 25 32 31 33 4 >> >> (my hard hand modifications) >> >> [ dihedrals ] ; impropers >> ; treated as propers in GROMACS to use correct AMBER analytical function >> ; i j k l func phase kd pn >> 5 13 11 12 4 180.00 43.93200 2 ; CA- N- >> C- O >> 11 15 13 14 4 180.00 4.60240 2 ; C- CA- >> N- H >> 15 23 21 22 4 180.00 43.93200 2 ; CA- N- >> C- O >> 21 25 23 24 4 180.00 4.60240 2 ; C- CA- >> N- H >> 25 32 31 33 4 180.00 43.93200 2 ; CA- OC1- >> C- OC2 >> >> I mean, if the parameters that are hiding in e.g. >> ...gromacs/top/amber99sb.ff >> could be showed in the top/itp file for human readers, that would be >> great. >> >> > 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 redmine.gromacs.org. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588
aGGG.pdb
Description: Protein Databank data
SPE.mdp
Description: Binary data
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