Chenlin Lu

5 Questions 7 Answers 0 Followers

Questions related from Chenlin Lu

How to deal with OXT atom in PDB file while using pdb2gmx in GROMACS?

I got an a fatal error "Atom OXT in residue ASP 174 was not found in rtp entry ASP with 9 atoms while sorting atoms." while using pdb2gmx in GROMACS. How could I deal with this OXT atom? What does...

12 December 2018 1,242 1 View

Why do I only get one curve in histo.xvg when doing umbrella sampling analysis with Gromacs?

I am working on umbrella sampling with Gromacs. The procedure is based on Justin's tutorial. When I ran gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal doing analysis, I got a...

05 May 2018 6,508 3 View

How could I only consider the LJ interaction (ignore the internal interaction inside g-C3N4) between g-C3N4 (which is fixed) and protein in Gromacs?

How could I only consider the Lennard-Jones interaction between g-C3N4 (which is fixed) and protein in Gromacs? I've added the LJ parameter of g-C3N4 into the ffnonbonded.itp file. I used gmx...

03 March 2018 10,037 0 View

How could I split a MD trajectory file (usually xtc file) into pieces (I'm using Gromacs)?

For example, if I got a xtc file whose simulation time is 50 ns, how could I split it into 10 sub-trajectories file of 5 ns?

03 March 2018 1,065 3 View

What should we do if some residues are missing in crystal structure (PDB) while doing MD simulation?

What should we do if some residues are missing in crystal structure (PDB) while doing MD simulation? Sometimes, some residues of the proteins show less electron density in crystal analysis and...

01 January 1970 663 9 View