Re: [gmx-users] g_mmpbsa: MM-PBSA method for GROMACS
Hi Rashmi, I am facing difficulty in installing the tool you mentioned g_mmpbsa. I am giving this command: ./configure --enable-gmx46 --with-gmx-include=/usr/local/gromacs/include --with-gmx-lib=/usr/local/gromacs/lib configure: error: Could not find /libgmx.a library file I found in my gromacs4.6.3 lib folder '/usr/local/gromacs/lib' the files are 'libgmx.so', 'libgmxana.so' etc.. instead of 'libgmx.a' or 'libgmxana.a'. Please suggest how do I get this files without hampering my installed gromacs as presently a number of programs are running. Thanks, Sucharita On Fri, Jun 13, 2014 at 10:32 PM, Rashmi rashk...@gmail.com wrote: Dear Prof. David van der Spoel, Thank you very much for considering g_mmpbsa for the GROMACS repository. We have a discussion on the same and will try to patch g_mmpbsa in the repository. Presently, we do not know how to integrate compilation procedure of g_mmpbsa with the GROMACS package as APBS libraries are required during compilation and Fortran compiler are required for the linking. Since I am travelling these days, hope we could able to work on the same in a month and so. With Regards Rashmi Kumari PhD Student School of Computational and Integrative Sciences Jawaharlal Nehru University New Delhi, India. On Tue, Jun 10, 2014 at 1:42 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2014-06-09 21:17, Rashmi wrote: Dear GROMACS users, We have developed a new tool, *g_mmpbsa* for GROMACS to carry out the MM-PBSA calculations. It uses APBS libraries for the Poisson-Boltzmann calculations. Features: - Include SASA, SAV and WCA -like non-polar models - It inherits threading (OpenMP) functions from APBS - Simultaneously calculate energy contribution s of residue s to binding Details of this tool are given in the following link: http://rashmikumari.github.io/g_mmpbsa/ Its implementation and testing are discussed in the following publication: http://pubs.acs.org/doi/abs/10.1021/ci500020m We would appreciate for suggestions regarding improvment of this tool. With Regards, Rashmi Kumari School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India. Why not upload a patch to http://gerrit.gromacs.org ? -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- With Regards, Rashmi Kumari Visting Student School of Chemistry and Molecular Biosciences (MD group) The University of Queensland St. Lucia, Brisbane, QLD 4072, Australia Contact No.- +61 434872368. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding lipid topology
Dear all, I want to simulate a membrane protein system. My membrane is composed of DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC topology from lipidbook website. Since DOPC and DEPC are isomers, can I use the topology of DOPC for DEPC also? Thank and regards Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to extend Amber FF parameters of Lipids
Dear gmx users, I would like to simulate lipid with a protein using AMBER force field. Have you any advice and useful links? Best regards, Batsaikhan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Regarding lipid topology
Of course, no. You need to adjust your topology (force field?) to distinguish between cis- and trans- states. Dr. Vitaly V. Chaban On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I want to simulate a membrane protein system. My membrane is composed of DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC topology from lipidbook website. Since DOPC and DEPC are isomers, can I use the topology of DOPC for DEPC also? Thank and regards Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to extend Amber FF parameters of Lipids
On 6/16/14, 6:47 AM, Batdorj Batsaikhan wrote: Dear gmx users, I would like to simulate lipid with a protein using AMBER force field. Have you any advice and useful links? http://md.chem.rug.nl/cgmartini/index.php/blog/269-jungle2 -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] dissociation of protein/peptide complex in the pdb derived from .xtc
dear users I have an .xtc file regarding an interacting protein/peptide complex. as i extract a pdb from this trajectory, i find the peptide separated from protein and in a position very far from it. i derived a pdb from .tpr file, to make sure that my starting structure is intact compared to the modeled structure that i used for preparing the .tpr file. i wondered whether the -pbc rot+trans and -center options of trajconv may help. but i still find the peptide far away from protein structure. is there any suggestion on how to fix this? regards, saman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] dissociation of protein/peptide complex in the pdb derived from .xtc
On 6/16/14, 9:05 AM, Saman Shahriyari wrote: dear users I have an .xtc file regarding an interacting protein/peptide complex. as i extract a pdb from this trajectory, i find the peptide separated from protein and in a position very far from it. i derived a pdb from .tpr file, to make sure that my starting structure is intact compared to the modeled structure that i used for preparing the .tpr file. i wondered whether the -pbc rot+trans and -center options of trajconv may help. but i still find the peptide far away from protein structure. is there any suggestion on how to fix this? http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
Dr. Justin Lemkul, Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? The final columns specify the new residue names that should be assigned to the residues only in the case that a special bond was created. You'll see from the existing Cys specifications that a residue named CYS (standard PDB nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but only if a special bond is created. The nomenclature exists because of the way the force fields work. In your case, you don't need to rename anything, so preserving the original residue names is the proper way to go. Of course, the answer to is this correct? is generally obtained by running it ;) 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 With the above specbond.dat file in the working directory, I attempted the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp and received this fatal error message (it is the same as the original): --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -Matthew Stancea -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/16/14, 12:31 PM, Matthew Stancea wrote: Dr. Justin Lemkul, Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like? The final columns specify the new residue names that should be assigned to the residues only in the case that a special bond was created. You'll see from the existing Cys specifications that a residue named CYS (standard PDB nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but only if a special bond is created. The nomenclature exists because of the way the force fields work. In your case, you don't need to rename anything, so preserving the original residue names is the proper way to go. Of course, the answer to is this correct? is generally obtained by running it ;) 3 CYS N 1 VAL C 1 0.132CYSVAL CYS SG 1 CYS SG 1 0.20CYS2CYS2 CYM SG 1 CYM SG 1 0.20CYS2CYS2 With the above specbond.dat file in the working directory, I attempted the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp and received this fatal error message (it is the same as the original): --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Your input coordinate file does not conform to the required nomenclature of the force field. The error message says it all. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
