> > Message: 8 > Date: Wed, 13 Feb 2013 08:28:00 -0500 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] md with multiple ligands > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <511b94e0.4040...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 2/13/13 5:24 AM, Ansuman Biswas wrote: >> >> Dear gromacs users, >> >> I wish to run a protein ligand md in Gromacs 4.5.3 with charmm force >> field. Its a dimeric protein with a MG ion and 2 ligands bound to two >> active sites. I wish to run the dimer and there would be 4 ligands. I >> generated the topology files (.itp) of ligands using SWISSPARAM. Before >> running the energy minimization I changed the topol.top file accordingly >> as mentioned in the SWISSPARAM website. I added all the itp files >> together.But while running GROMPP I got an error message like, >> >> >> WARNING 1 [file ADP.itp, line 24]: >> Overriding atomtype NPYL >> >> >> WARNING 2 [file ADP.itp, line 25]: >> Overriding atomtype C5A >> >> >> WARNING 3 [file ADP.itp, line 26]: >> Overriding atomtype N5B >> >> >> WARNING 4 [file ADP.itp, line 27]: >> Overriding atomtype C5B >> >> >> WARNING 5 [file ADP.itp, line 28]: >> Overriding atomtype CB >> >> >> WARNING 6 [file ADP.itp, line 29]: >> Overriding atomtype NPYD >> >> >> WARNING 7 [file ADP.itp, line 30]: >> Overriding atomtype PO4 >> >> >> WARNING 8 [file ADP.itp, line 31]: >> Overriding atomtype O2CM >> >> >> WARNING 9 [file ADP.itp, line 32]: >> Overriding atomtype OR >> >> >> WARNING 10 [file ADP.itp, line 33]: >> Overriding atomtype CR >> >> >> WARNING 11 [file ADP.itp, line 34]: >> Overriding atomtype NC=C >> >> >> WARNING 12 [file ADP.itp, line 35]: >> Overriding atomtype HCMM >> >> >> WARNING 13 [file ADP.itp, line 36]: >> Overriding atomtype HNCO >> >> >> WARNING 14 [file ADP.itp, line 37]: >> Overriding atomtype HOCO >> >> >> WARNING 15 [file ADP.itp, line 38]: >> Overriding atomtype HOR >> >> >> WARNING 16 [file ADP.itp, line 43]: >> Overriding atomtype PO4 >> >> >> WARNING 17 [file ADP.itp, line 44]: >> Overriding atomtype O2CM >> >> >> WARNING 18 [file ADP.itp, line 45]: >> Overriding atomtype OR >> >> >> WARNING 19 [file ADP.itp, line 46]: >> Overriding atomtype CR >> >> >> WARNING 20 [file ADP.itp, line 48]: >> Overriding atomtype HCMM >> >> >> WARNING 21 [file ADP.itp, line 49]: >> Overriding atomtype HOR >> >> >> WARNING 22 [file ADP.itp, line 50]: >> Overriding atomtype HOCO >> >> >> WARNING 23 [file ADP.itp, line 52]: >> Overriding atomtype NC=O >> >> >> WARNING 24 [file ADP.itp, line 53]: >> Overriding atomtype C=O >> >> >> WARNING 25 [file ADP.itp, line 54]: >> Overriding atomtype N=C >> >> >> WARNING 26 [file ADP.itp, line 55]: >> Overriding atomtype C=C >> >> >> WARNING 27 [file ADP.itp, line 56]: >> Overriding atomtype PO4 >> >> >> WARNING 28 [file ADP.itp, line 57]: >> Overriding atomtype O2CM >> >> >> WARNING 29 [file ADP.itp, line 58]: >> Overriding atomtype OR >> >> >> WARNING 30 [file ADP.itp, line 59]: >> Overriding atomtype CR >> >> >> WARNING 31 [file ADP.itp, line 60]: >> Overriding atomtype O=C >> >> >> WARNING 32 [file ADP.itp, line 61]: >> Overriding atomtype HCMM >> >> >> WARNING 33 [file ADP.itp, line 62]: >> Overriding atomtype HOCO >> >> >> WARNING 34 [file ADP.itp, line 63]: >> Overriding atomtype HOR >> >> >> WARNING 35 [file ADP.itp, line 64]: >> Overriding atomtype HOCC >> >> Generated 25425 of the 25425 non-bonded parameter combinations >> Generating 1-4 interactions: fudge = 1 >> Generated 22285 of the 25425 1-4 parameter combinations >> >> ------------------------------------------------------- >> Program grompp, VERSION 4.5.3 >> Source code file: toppush.c, line: 1071 >> >> Fatal error: >> Atoms in the .top are not numbered consecutively from 1 (rather, atomnr >> = >> 1, while at->nr = 40) >> >> I know that the problem is related to the merging of 4 itp files. >> Please let me how I should do that. >> > > The ligands probably use common atom types and each .itp file likely has > an > [atomtypes] directive that introduces these new types. Probably the > easiest > thing to do is create a merged [atomtypes] directive that lists all of the > necessary atom types so you don't list them separately in each file. One > approach that I have used in the past is to create an .itp file that only > has > atom types in it, then call something like: > > #include "charmm27.ff/forcefield.itp" > > ; only has [atomtypes] > #include "my_ligand_atomtypes.itp" > > ; these don't introduce [atomtypes] any more > #include "ligand1.itp" > #include "ligand2.itp" > > -Justin But according to SWISSPARAM website I can only add one ligand.itp file. So, is it possible to add ligand1 and ligand2 itp files?
Will it be ok if I merge all the ligand pdbs and then get the combined itp file using that from SWISSPARAM and follow the protocol for one ligand? Ansuman > > -- > ======================================== > > 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 > > ======================================== > > > ------------------------------ > > -- > 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! > > End of gmx-users Digest, Vol 106, Issue 68 > ****************************************** > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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
