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
Hi Acoot,
Read the tutorial. It's explained there... Mind that that tutorial was
written for an earlier version of Gromacs and some things have changed. The
names of ions, for instance.
Cheers,
Tsjerk
On Mar 19, 2012 6:40 AM, Acoot Brett acootbr...@yahoo.com wrote:
Dear All,
The problem
Dear All,
I am practicing the on-line tutorial
http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/.
In the step mdrun -v -deffnm 1LW9-EM-solvated of Energy minimization of the
solvated system, it says
Converged to machine precision , but not to the requested precision Fmax 1.
Before
Acoot Brett wrote:
Dear All,
I am practicing the on-line tutorial
http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/.
In the step mdrun -v -deffnm 1LW9-EM-solvated of Energy minimization
of the solvated system, it says
Converged to machine precision , but not to the requested
Dear All,
The problem really occurs in the ion addition step.
In order to keep 0.1 M ion concentration, 20 Na+ and 20 C1- were added. In
order to keep 0 charge, 8 Cl- were added.
From the .gro file, 48 water (72 H and 48 O) were deleted in order to add the
38 charges, which makes there was
hello
I m unable to update the [ molecules ] directive of topol_pope.top .
grompp -f minim.mdp -c system_inflated.gro -p topol_pope.top -o em1.tpr
Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 20782)
does not match topology (topol_pope.top, 37867)
Quoting shikha agarwal shikhaiiit...@gmail.com:
hello
I m unable to update the [ molecules ] directive of topol_pope.top .
grompp -f minim.mdp -c system_inflated.gro -p topol_pope.top -o em1.tpr
Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 20782)
Dear ALL,
I am running simulation for the drug enzyme complex using Gromacs with
gromacs96(43a2)forcefield. After generating waterbox around my protein,
when I am running grompp command (before energy minimization) I am getting
following error:
I have already asked about this but I think maybe I did not give enough
information so I made the following page:
http://cs86.com/CNSE/SWNT.htm
It outlines every step I have taken and where I am stuck is at the end with
grompp when it spits out the following error:
Christopher Stiles wrote:
I get the following when running grompp:
-bash-3.00$ grompp -f mdout_test.mdp -c SWNT_6_6_144.gro -p
SWNT_6_6_144.top -o
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
I get the following when running grompp:
-bash-3.00$ grompp -f mdout_test.mdp -c SWNT_6_6_144.gro -p SWNT_6_6_144.top
-o
:-) G R O M A C S (-:
God Rules Over Mankind, Animals, Cosmos and Such
:-) VERSION
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