[gmx-users] Constructing covalent bond between protein-ligand complex

ting 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

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 f

[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 -2.00