[gmx-users] problem in multichain protein solvation

I tried to solvate an assembly of amyliod peptides (16 peptide), using editconf and genbox respectively as follow, editconf -f rotated.gro -box 76 6 6 -center 0 0 0 -o rotated-box then, genbox -cs ffamber_tip3p.gro -cp rotated-box -p fragment -o sol when, I tried to visualize the protein using

[gmx-users] (no subject)

Hi, everybody, I tried to use pdb2gmx program to obtain .top& .gro files but I eceived the following error message Fatal error: Atom HB3 in residue ARG 1 not found in rtp entry with 24 atoms while sorting atoms. Maybe different protonation state. Remove this hydrogen or

[gmx-users] pdb2gmx

Dear All, I tried to use the following command line pdb2gmx -f -i brady.pdb -o brady.gro -p brady.top -ignh But I get the following error massage File input/output error: eiwit.pdb So I tried to modify aminoacides.dat to include all the required aminoacids residues but , I failed because the

[gmx-users] pdb2gmx

Dear All, I tried to use the following command line pdb2gmx -f -i brady.pdb -o brady.gro -p brady.top -ignh But I get the following error massage File input/output error: eiwit.pdb So I tried to modify aminoacides.dat to include all the required aminoacids residues but , I failed because the

[gmx-users] error coordinates in .gro donnot match .top

Hi, all when I want to use gromacs preprocessor grompp to obtain .tpr to use in the energy minimization as follow grompp -f minim.mdp -c bradywaterbox.gro -p brady.top -o minimbrady.tpr I got the following error message Fatal error: number of coordinates in coordinate file (bradywaterbox.gro, 6

[gmx-users] problems with gromacs preprocessor

Dear All, when I want to use grompp program grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr I got the following error message Fatal error: [ file "spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) So I tried to modify the topology file b

[gmx-users] problems with gromacs preprocessor

Dear All, when I want to use grompp program grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr I got the following error message Fatal error: [ file "spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) So I tried to modify the topology file b

[gmx-users] problems with gromacs preprocessor

Dear All, when I want to use grompp program grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr I got the following error message Fatal error: [ file "spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) So I tried to modify the topology file b

[gmx-users] using mdrun in the supercomputer

Dear gromacs users, I tried to make MD simulation using mdrun in the super computer by using the following script: #!/bin/sh #$ -cwd –V #$ -l h_rt=1:00:00 #$ -pe mx* 4 export DO_PARALLEL=”/usr/local/sge6.0/mpi/myrinet/sge_mpirun” export gromacs=/apps/gromacs/64/3.3.1-ffamber20080701/bin $ DO

[gmx-users] center the protein to the origin

Hi, I am simulating a protein in water. But I have forgotten to center the protein from the beginning to the origin. So, is it possible to center the protein to the origin in the trajectory file? And if it is not possible, how can obtain the atomic positions independent of the center of mass,

[gmx-users] energy file with g_dipoles

Hi, I have a question regarding g_dipoles. Why does g_dipoles give completely different results of the total dipole moment, when I add or omit the energy file? and which is correct? I mean by providing the energy file or not? and how come I use the energy file when I want to calculate the dipole