Justin, Regarding the charges you mention, what do you think about RESP charges for this kind of compounds (drugs) parameterization?
Best wishes Esteban -- On Mon, Nov 15, 2010 at 11:12 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > Just the $0.02 that I always seem to contribute in these types of > discussions - the topology you have shown below contains some likely > problems. The charges (and massive charge group size) can lead to > artifacts. We've got a paper due out soon about the implications of > incorrect charges, but I would advise you that this topology should *not* be > used for production simulation. You'd be better off spending the time to > properly parameterize the molecule rather than run a bunch of simulations > and get questionable (at best) or wrong (at worst) results. > > http://www.gromacs.org/Documentation/How-tos/Parameterization > > -Justin > > Olga Ivchenko wrote: > >> >> Hey Vitaly, >> >> Thank you for your reply. Here is the files: >> >> *itp:* >> ; ; ; This file was generated by PRODRG version >> AA081006.0504 >> ; PRODRG written/copyrighted by Daan van Aalten >> ; and Alexander Schuettelkopf >> ; ; Questions/comments to d...@davapc1.bioch.dundee.ac.uk<mailto: >> d...@davapc1.bioch.dundee.ac.uk> >> >> ; ; When using this software in a publication, cite: >> ; A. W. Schuettelkopf and D. M. F. van Aalten (2004). >> ; PRODRG - a tool for high-throughput crystallography >> ; of protein-ligand complexes. >> ; Acta Crystallogr. D60, 1355--1363. >> ; ; >> [ moleculetype ] >> Name nrexcl >> DRG 3 >> >> [ atoms ] >> ; nr type resnr resid atom cgnr charge mass >> 1 OM 1 DRG OXT 1 -0.701 15.9994 2 >> C 1 DRG C 1 0.402 12.0110 3 OM 1 DRG >> O 1 -0.701 15.9994 4 CH2 1 DRG CA 2 >> 0.185 14.0270 5 N 1 DRG N 2 0.468 14.0067 >> 6 CH3 1 DRG CAG 2 0.201 15.0350 7 >> C 1 DRG CAH 2 0.377 12.0110 8 NZ 1 DRG >> NAE 2 -0.163 14.0067 9 H 1 DRG HA6 2 >> 0.023 1.0080 10 H 1 DRG HAE 2 0.024 1.0080 >> 11 NZ 1 DRG NAD 2 -0.163 14.0067 12 >> H 1 DRG HA5 2 0.024 1.0080 13 H 1 DRG >> HAD 2 0.024 1.0080 >> [ bonds ] >> ; ai aj fu c0, c1, ... >> 2 1 2 0.125 13400000.0 0.125 13400000.0 ; C OXT 2 >> 3 2 0.125 13400000.0 0.125 13400000.0 ; C O 2 4 2 >> 0.153 7150000.0 0.153 7150000.0 ; C CA 5 4 2 0.147 >> 8710000.0 0.147 8710000.0 ; N CA 5 6 2 0.147 >> 8710000.0 0.147 8710000.0 ; N CAG 5 7 2 0.134 >> 10500000.0 0.134 10500000.0 ; N CAH 7 8 2 0.134 >> 10500000.0 0.134 10500000.0 ; CAH NAE 7 11 2 0.134 >> 10500000.0 0.134 10500000.0 ; CAH NAD 8 9 2 0.100 >> 18700000.0 0.100 18700000.0 ; NAE HA6 8 10 2 0.100 >> 18700000.0 0.100 18700000.0 ; NAE HAE 11 12 2 0.100 >> 18700000.0 0.100 18700000.0 ; NAD HA5 11 13 2 0.100 >> 18700000.0 0.100 18700000.0 ; NAD HAD >> [ pairs ] >> ; ai aj fu c0, c1, ... >> 1 5 1 ; OXT N 2 >> 6 1 ; C CAG 2 7 1 >> ; C CAH 3 5 1 >> ; O N 4 8 1 >> ; CA NAE 4 11 1 >> ; CA NAD 5 9 1 >> ; N HA6 5 10 1 >> ; N HAE 5 12 1 ; N >> HA5 5 13 1 ; N HAD >> 6 8 1 ; CAG NAE 6 11 >> 1 ; CAG NAD 8 12 1 >> ; NAE HA5 8 13 1 >> ; NAE HAD 9 11 1 >> ; HA6 NAD 10 11 1 >> ; HAE NAD >> [ angles ] >> ; ai aj ak fu c0, c1, ... >> 1 2 3 2 126.0 770.0 126.0 770.0 ; OXT C >> O 1 2 4 2 117.0 635.0 117.0 635.0 ; OXT C >> CA 3 2 4 2 117.0 635.0 117.0 635.0 ; O >> C CA 2 4 5 2 109.5 520.0 109.5 520.0 ; C >> CA N 4 5 6 2 121.0 685.0 121.0 685.0 ; >> CA N CAG 4 5 7 2 122.0 700.0 122.0 700.0 ; >> CA N CAH 6 5 7 2 117.0 635.0 117.0 635.0 >> ; CAG N CAH 5 7 8 2 120.0 670.0 120.0 >> 670.0 ; N CAH NAE 5 7 11 2 120.0 670.0 120.0 >> 670.0 ; N CAH NAD 8 7 11 2 120.0 670.0 120.0 >> 670.0 ; NAE CAH NAD 7 8 9 2 120.0 390.0 120.0 >> 390.0 ; CAH NAE HA6 7 8 10 2 120.0 390.0 >> 120.0 390.0 ; CAH NAE HAE 9 8 10 2 120.0 445.0 >> 120.0 445.0 ; HA6 NAE HAE 7 11 12 2 120.0 >> 390.0 120.0 390.0 ; CAH NAD HA5 7 11 13 2 120.0 >> 390.0 120.0 390.0 ; CAH NAD HAD 12 11 13 2 120.0 >> 445.0 120.0 445.0 ; HA5 NAD HAD >> [ dihedrals ] >> ; ai aj ak al fu c0, c1, m, ... >> 2 1 3 4 2 0.0 167.4 0.0 167.4 ; imp C OXT >> O CA 5 4 6 7 2 0.0 167.4 0.0 167.4 ; imp >> N CA CAG CAH 7 5 8 11 2 0.0 167.4 0.0 167.4 ; >> imp CAH N NAE NAD 8 7 10 9 2 0.0 167.4 0.0 >> 167.4 ; imp NAE CAH HAE HA6 11 7 13 12 2 0.0 167.4 >> 0.0 167.4 ; imp NAD CAH HAD HA5 5 4 2 1 1 0.0 >> 1.0 6 0.0 1.0 6 ; dih N CA C OXT 2 4 5 7 1 >> 180.0 1.0 6 180.0 1.0 6 ; dih C CA N CAH 11 7 5 >> 4 1 180.0 33.5 2 180.0 33.5 2 ; dih NAD CAH N CA 5 >> 7 8 10 1 180.0 33.5 2 180.0 33.5 2 ; dih N CAH NAE >> HAE 5 7 11 13 1 180.0 33.5 2 180.0 33.5 2 ; dih N >> CAH NAD HAD >> >> >> >> >> >> >> >> *And top. I am prettu sure this file is wrong. And I do not know yet how >> to modify it correctly: >> >> * >> >> ; >> ; File 'creatine.top' was generated >> ; By user: onbekend (0) >> ; On host: onbekend >> ; At date: Mon Nov 15 13:24:44 2010 >> ; >> ; This is your topology file >> ; it was generated using program: >> ; pdb2gmx - version 4.5-beta2 >> ; with command line: >> ; pdb2gmx -f creatine_all_hyd_PRODRGBeta.pdb -o creatine.gro -p >> creatine.top >> ; >> >> #include "creatine.itp" >> #include "gromos43a1.ff" >> >> >> ; Include forcefield parameters >> ;#include "gromos43a1.ff/forcefield.itp" >> >> ;"gromos43a1.ff/creatine.itp" >> >> >> ;[ system ] >> >> ;[ molecules ] >> ;DRG 3 >> >> >> >> >> 2010/11/15 Vitaly Chaban <vvcha...@gmail.com <mailto:vvcha...@gmail.com>> >> >> >> Hey, Olga - >> >> > Also please can you tell me where can I get "ffgmx.itp" file? >> >> /$gromacs_folder/share/gromacs/top/ffgmx.itp as well as all other >> standard topology files are there. >> >> By trying to run md I am getting an error: Fatal error: >> > moleculetype UNK is redefined >> >> Please post you top and itp files here. Looks like you have 2 creatine >> molecules in your topology right now. >> >> Good luck! >> >> Vitaly >> >> >> >> >> > I still have troubles of starting running md for creatine. For >> which I >> > created topology using PRODRG programm. >> > The only difference between creatine.top and creating.itp is that >> creatine >> > top has additional lines: >> > #include "ffgmx.itp" >> > #include "creatine.itp" >> > >> > Also please can you tell me where can I get "ffgmx.itp" file? >> > >> > By trying to run md I am getting an error: Fatal error: >> > moleculetype UNK is redefined >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > 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 > Please search the archive at > 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 >
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