[gmx-users] help---How to define new residue in GROMACS?

My problem is How to define new residue in GROMACS? i have made a 3-d structure model for a protein based on a template protein，which has a heme group. befor runing the gromacs molecular simulation,i must define the heme group as a new residue,How to define new residue in GROMACS? thanks !_

[gmx-users] HELP:Fatal error: There were 1 error(s) processing your input

Hi all: I want to start simulation of protein that has heme group(FE).After learning the force field paremeter ,i add heme parameters to the force field's .rtp and .hdb file,and define a new bond . i operated the gromacs command as followed. 1 pdb2gmx -ignh -ff G43a1 -f ffg43a1.pdb -o ff

[gmx-users] error:Segmentation fault

Hello everyone I am doing MD on a protein, and everything including the EM seems to go well. When I start to do the position restrained MD (or even directly the MD without doing the PR MD), I get a "Segmentation fault". when a doing EM,I set nsteps = 500,because i just want to go though the

[gmx-users] HEME-cysteine gromacs simulation

HI all: I want to run a simulation with heme group(cytochrome p450). i have made a 3-d structure model for a cytochrome p450 .I use the ffG43a1 force field,someone told me that i need both suitable parameters for your desired force field, and then to construct a correct topology. I read lots o

[gmx-users] Re: HEME-cysteine gromacs simulation (zimohmily)

Thanks both Mark and chris.ne...@utoronto.ca 's advises. Listening to these words of yours,is better than learning for ten years. Most people uses the AMBER force field to run HEME simulation,I should focus on suitable force field and associated correct parameters.thanks > 1. Re: HEME-cystei