Thanks Justin, you were right. In the end gmxdump helped to clear some doubts but I wished it would be less painfully.
Cheers, Alan On 22 May 2012 12:36, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > On 5/22/12 12:46 PM, Alan wrote: > >> 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? >> >> > Make sure you're looking at types, not names. The type sequence here is > H-N3-CT-HP, which I think is mapped to this dihedral: > > X CT N3 X 9 0.0 0.65084 3 ; JCC,7,(1986),230 > > Running gmxdump on the .tpr file will show it for sure; I had assumed it > would be in the post-processed topology as well, but I guess not. > > -Justin > > Thanks, >> >> Alan >> >> On 21 May 2012 18:50, Justin A. Lemkul <jalem...@vt.edu >> <mailto: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 <http://redmine.gromacs.org>. >> >> -Justin >> >> -- >> ==============================**__========== >> >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <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 <mailto: >> gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <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> >> >> >> <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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> >> <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 >> >> > -- > ==============================**========== > > 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
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