Amanpreet Kaur

9 Questions 11 Answers 0 Followers

Questions related from Amanpreet Kaur

How to get RMSF graph against the time scale on x axis in Amber 20?

Hlo All I obtained the rmsf graph by using the command line cpptraj parm solv_7zzt_chainb_noh.com1_no_water.prmtop trajin nowatermd_7zzt_chainb_noh.com2.nc list trajin autoimage atomicfluct out...

20 October 2022 7,404 2 View

ERROR: max pairlist cutoff must be less than unit cell max sphere radius! in amber 20 GPU based ?

Hy everyone!!!! I am running the MD command """"""pmemd.cuda.MPI -O -i mD.in -o mD.out -p solv_6lu7.prmtop -c equiD.ncrst -r mD.rst7 -x mD.nc -ref equiD.ncrst -AllowSmallBox """""""""" on amber...

19 August 2022 2,918 0 View

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 1,561 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 7,127 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 8,303 3 View

Error : Atom HN1 in residue PRO 4 was not found in rtp entry PRO with 9 atoms while sorting atoms?

I was giving first command of gromacs, I selected groos forcefield no. 14 the united atom charge but after that I encountered the error while funning the command pdb2gx that "Atom HN1 in residue...

30 April 2022 6,257 0 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 5,106 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 5,771 3 View

How to convert rmsd graph containing frames on x axis into time in ns?

I have obtained graph containing 5000 frames on x axis I want to convert it into time i.e.100 ns. I am using amber 20 which is GPU based.

01 January 1970 2,978 0 View