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
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
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
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
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
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
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
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
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
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,
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
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