Question: using gromacs to run molecular dynamic simulation of SNP
0
gravatar for arronslacey
3.3 years ago by
arronslacey240
United Kingdom
arronslacey240 wrote:

Hi - I would like to run MD simulations on mutated proteins (misense SNPs in particular). I have used a fasta format file with the misense mutation embedded in the sequence as input to I-TASSER. I-TASSER has in turn produces 5 models that I can choose to send to GROMACS. I have used

gmx pdb2gmx -f mymodel.pdb -o mymodel.gro

to get my mutation pdb file into .gro format.

 

I am currently a bit stuck as to how I then take this new .gro file and perform md simulation using GROMACS. I understand I can use

 

gmx mdrun <options>

 

however there doesn't seem to be an option use my .gro file as input to mdrun. I suspect I am missing some intermediate steps.

 

Could someone point my in the right direction? Thanks very much.

snp molecular dynamics gromacs md • 1.2k views
ADD COMMENTlink written 3.3 years ago by arronslacey240
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2116 users visited in the last hour