[gmx-users] md with multiple ligands
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. thanking you, with regards, Ansuman Biswas C/O Prof K.Sekar Dept.of Physics Indian Institute of Science Bangalore:560012 India -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-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
[gmx-users] Re: gmx-users Digest, Vol 106, Issue 68
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
[gmx-users] md with multiple ligands
Original Message Subject: Re: gmx-users Digest, Vol 106, Issue 68 From:ansuman@localhost Date:Thu, February 14, 2013 10:16 am To: gmx-users@gromacs.org -- 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
