using gromacs to run molecular dynamic simulation of SNP
0
0
Entering edit mode
5.5 years ago
arronslacey ▴ 280

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.

gromacs SNP md molecular dynamics • 1.8k views
ADD COMMENT

Login before adding your answer.

Traffic: 2192 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6