Sandip Dolui

4 Questions 7 Answers 0 Followers

Questions related from Sandip Dolui

Can someone help me get rid of warnings when I run Autogrid4 from terminal?

When I run Autogrid4 from terminal I get a warnings like Found an H-bonding atom with three bonded atoms, atom serial number 479 Found an H-bonding atom with three bonded atoms, atom serial...

12 January 2015 6,929 6 View

Gromacs MD simulation of protein-ligand complex - how can I generate a o nvt.tpr file?

I want to run an MD simulation for Protein-ligand complex and following Gromacs tutorial of Justin Lemkul Department of Biochemistry, Virginia Tech. I have successfully generated "jz4.gro" and...

12 March 2014 568 10 View

How to correct the number of coordinates in coordinate file if it does not match the topology in Gromacs?

I ran gromacs with command: grompp -f ions.mdp -c protein a_solv.gro -p topol.top -o ions.tpr. and yielded a Fatal error: Correct the number of coordinates in coordinate file (protein a.gro,...

21 February 2014 4,850 11 View

Anyone have experience with how to write the command prompt in Gromacs for two similar peptides in water with the presence of heme?

Can anybody give an advice?

13 February 2014 8,443 9 View