Amanpreet Kaur

5 Questions 7 Answers 0 Followers

Questions related from Amanpreet Kaur

Should the ligand be inside the protein after the complex combine command in amber provided that ligand was not in real protein PDBID?

I am giving commands for complex formation "COM = combine {complex PYR} savepdb COM 1ua7_noh.com.pdb " of protein and ligand while checking its pdb in Discovery studio I checked that the ligand is...

28 June 2022 1,555 6 View

Error in amber command?

Hy I was giving tfollowing the commands tleap source leaprc.protein.ff14SB MOL=loadpdb 1ua7.pdb savepdb MOL 1ua7-amb.pdb MOL2=loadpdb 1ua7-amb.pdb charge MOL2 source leaprc.water.tip3p solvateBox...

16 June 2022 7,118 1 View

Error in gromacs command?

I was giving the command gmx mdrun -v -deffnm em while doing the energy minimization step but i encountered the error . Fatal error: There is no domain decomposition for 8 ranks that is...

04 May 2022 8,290 3 View

How to run MD in gromacs from docking with two ligands in pyrx software?

I have done docking of 2 ligands with pyrx and selected two best poses with maestro but now I want pdb file of that complex bcz in gromacs the first command is pdb2gmx .So how to get pdb file of...

29 April 2022 5,098 3 View

Error: Group Protein_benz referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom ?

I gave the command gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr while doing the MD run in gromacs but I got the above error .But now I am in dilemma where the...

19 April 2022 5,759 3 View