Dear gmx users,
I have .pdb file. This .pdb file represents a dimer protein. When I try to
generate a topology file of it, GROMACS asks for terminals one by one, ( 2
N-terminals, 2 C-terminals ) . But after rotation of protein, 2 terminals are
lost and the total charge is incorrect.
The pdb
Yes it will work ..
Just at the time of mdrun add -cpi cpt ( prvious cpt file )
With best wishes and regards..!!
On Sun, Sep 30, 2012 at 8:48 AM, Acoot Brett acootbr...@yahoo.com wrote:
Dear All,
for my original MD, based on mdp file the total time is 500 ps. After it
finished, I have
Hi Shima,
How did you rotate the structure? Probably the TER records got lost in
the process.
Cheers,
Tsjerk
On Sun, Sep 30, 2012 at 9:23 AM, Shima Arasteh
shima_arasteh2...@yahoo.com wrote:
Dear gmx users,
I have .pdb file. This .pdb file represents a dimer protein. When I try to
The input file has TER between 2 monomers.
The command which I use is:
#editconf -princ -rotate 0 60 0 -f protein.pdb -o protein-rotate.gro
After that, I use editconf to convert .gro to .pdb file:
#editconf -f protein-rotate.gro -o protein.pdb
The residue numbers after 10th one of output pdb
Thank you for your immediate reply..
I need the xvg graph that will tell me the density of water in between the
protein with respect to time .
g_densmap not give such out put..
Sol please would you tell me how to do it ???
How to select the Sol that are only in between the protein ??
Thank
On 9/29/12 11:47 PM, Elie M wrote:
Dear all,
I am trying to minimize the energy of a polymer system I have. I have successfully
modified the n2t file to include force fields for atoms that were not present. However
now I am using grompp before using mdrun (to minimize). However I have a
On 9/30/12 1:06 PM, venkatesh s wrote:
Respected gromacs users
now iam buliding the simulation system
for protein + peptide simulation (manually insert the peptide into the
protein structure file after the TER )
following commands i used here
1. pdb2gmx -f
Please keep all Gromacs-related correspondence on the gmx-users mailing list. I
am CC'ing this message there and would ask that all further correspondence be
posted to the list so that you can benefit from commentary from the entire
community.
See comments below.
On 9/30/12 2:09 PM, Chris
Dear all,
Maybe this error has been discussed before; I have checked previous messages on
it but i could not resolve it. I have done a modified version of the oplsaa
forcefield which I have called ffoplsaamod.n2t. The top file was created
successfully. However when I run grompp, I get the
Hi everyone,
I am doing a DNA simulation in a long simulation box (the lengthen of z is
much larger than x and y). So I want to constrain the DNA molecule lying
along the z axis. But I don't know how to realize this in GROMACS.
Actually I notice there is orientation restraints in 4.3.5 of GMX
Hi everyone,
I am doing a DNA simulation in a long simulation box (the lengthen of z is
much larger than x and y). So I want to constrain the DNA molecule lying
along the z axis. But I don't know how to realize this in GROMACS.
Actually I notice there is orientation restraints in 4.3.5 of GMX
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