Re: [gmx-users] Protein-Ligand complex Implicit simulation
Please remember to use a proper subject line and don't reply to the whole digest. On 5/20/15 9:54 AM, sunita gupta wrote: Thanks Justin for your reply Below is the file where I added h1 parameters in gbsa.itp...In the same way I added the parameters for all the possible atomtypes from gaff ff [ implicit_genborn_params ] ; atype sar st pi gbr hct ;Br 0.1 1 10.125 0.85 ; H C0.1721 1.5540.18750.72 ; C CA 0.18 1 1.0370.18750.72 ; C CB 0.1720.012 1.5540.18750.72 ; C CC 0.1721 1.5540.18750.72 ; C CN 0.1720.012 1.5540.18750.72 ; C CR 0.18 1 1.0730.18750.72 ; C CT 0.18 1 1.2760.190 0.72 ; C CV 0.18 1 1.0730.18750.72 ; C CW 0.18 1 1.0730.18750.72 ; C C* 0.1720.012 1.5540.18750.72 ; C H0.1 1 10.115 0.85 ; H HC 0.1 1 10.125 0.85 ; H H1 0.1 1 10.125 0.85 ; H HA 0.1 1 10.125 0.85 ; H H4 0.1 1 10.115 0.85 ; H H5 0.1 1 10.125 0.85 ; H HO 0.1 1 10.105 0.85 ; H HS 0.1 1 10.125 0.85 ; H HP 0.1 1 10.125 0.85 ; H N0.1551 1.0280.17063 0.79 ; N NA 0.1551 1.0280.17063 0.79 ; N NB 0.1551 1.2150.17063 0.79 ; N N2 0.16 1 1.2150.17063 0.79 ; N N3 0.16 1 1.2150.16250.79 ; N O0.15 1 0.9260.148 0.85 ; O OH 0.1521 1.0800.15350.85 ; O O2 0.17 1 0.9220.148 0.85 ; O S0.18 1 1.1210.17750.96 ; S SH 0.18 1 1.1210.17750.96 ; S *h1 0.1 1 10.139 0.85 ; H * The error is Couldn't find topology match for atomtype h1 Aborted (core dumped) A quick look through the code suggests that when grompp parses the gbsa.itp file and finds h1 it cannot find that atom type in the force field, so something outside of the gbsa.itp file itself is the problem, e.g. you're providing a type that doesn't exist or otherwise isn't used. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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] Protein-Ligand complex Implicit simulation
Hello Everyone, I am trying to do protein-ligand complex simulation with implicit solvent parameters using gromacs. As, ligand parameters are not present in gbsa.itp, I added all the possible atomtypes and their van der wall radii from gaff ff and also managed to get get the HCT paremeters. Still its giving errorsAnyone please suggest me how to proceed further. Thanks in Advance -- -- SUNITA GUPTA Senior Research Fellow Bioinformatics Centre Jawaharlal Nehru University New Delhi- 110067 Email- sunita@gmail.com -- 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] Protein-Ligand complex Implicit simulation
On 5/18/15 3:35 PM, sunita gupta wrote: Hello Everyone, I am trying to do protein-ligand complex simulation with implicit solvent parameters using gromacs. As, ligand parameters are not present in gbsa.itp, I added all the possible atomtypes and their van der wall radii from gaff ff and also managed to get get the HCT paremeters. Still its giving errorsAnyone please suggest me how to proceed further. Without knowing what errors you're getting, the only answer is you're still doing something wrong. Ask a generic question, get a generic answer :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
