[gmx-users] Constructing covalent bond between protein-ligand complex
Dear all, Guided by gmxusers' list I have used gmx_top_tools.tgz (http://www.gromacs.org/Downloads/User_contributions/Other_software) to prepare the protein-ligand complex linked by a covalent bond. Unfortunately the tool renumtop is detecting a duplicate atom but not updating its number. Only gives an error message: ; ERROR: duplicate atom label '4968' for atom #4968 (already used for atom #4968) I used the command ./renumtop topol_Protein_chain_A.itp topol_Chain_B.itp. may be I am doing something wrong. Please help. Suman Nandy Suman Kumar Nandy Senior Research Fellow Department of Biochemistry Biophysics University of Kalyani Kalyani-741235 India.-- 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] Problem with FE-Cys covalent bond
Dear gromacs users, I have a problem regarding the simulation of Fe4S4 cluster attached to CYS of a protein using opls ff. I editted the aminoacids.rtp file as like this. [ SF4 ] ... [ atoms ] FE1 opls_966 2.500 1 FE2 opls_967 2.500 1 FE3 opls_968 2.500 1 FE4 opls_969 2.500 1 S1 opls_970 -2.000 1 S2 opls_971 -2.000 1 S3 opls_972 -2.000 1 S4 opls_973 -2.000 1 [ bonds ] FE1 S1 FE1 S2 FE1 S3 FE2 S1 FE2 S2 FE2 S4 FE3 S2 FE3 S3 FE3 S4 FE4 S1 FE4 S2 FE4 S3 and also atomtypes.atp as opls_966 55.84500 ; FE1: HEME opls_967 55.84500 ; FE2: HEME opls_968 55.84500 ; FE3: HEME opls_969 55.84500 ; FE4: HEME opls_970 32.06000 ; S1: S opls_971 32.06000 ; S2: S opls_972 32.06000 ; S3: S opls_973 32.06000 ; S4: S I have also added a line to specbond.dat regarding the SG-FE covalent bond. But while running the pdb2gmx command, (withouit any error) it just adds a H with SG (where the FE to bind)and there is no information on SG-FE bond in topology file. Please help. Suman Kumar Nandy Senior Research Fellow Department of Biochemistry Biophysics University of Kalyani Kalyani-741235 India.-- 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
Re: [gmx-users] Problem in Disulfide Bond between different chain!
use -chainsep interactive option in pdb2gmx. Suman On Wed, 11 Jan 2012 16:42:12 +0530 wrote Dear all: I want to do a simulation using a dimer, but the system is connected by 2 disulfide bonds between A-chain and B-chain. I have produced topology file for protein with pdb2gmx using AMBER99SB forcefield. In order to bond disulfide bonds I using flag -ss. If I do not delete the TER line between A-chain and B-chain in .pdb file, the program pdb2gmx can not recognize the disulfide bonds between A-chain and B-chain. But if I delete the TER line, I get the two bonds successfully. There would be another problem, the C-terminal of A-chain and the N-terminal will be bonded in the .top file. How should I do? I am using gromacs 4.5.4! Sincerely yours, Xianwei Wang -- 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 Suman Kumar Nandy Senior Research Fellow Department of Biochemistry Biophysics University of Kalyani Kalyani-741235 India.-- 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
