hello:
I found the script charmm2gromacs-pvm.py
http://www.gromacs.org/@api/deki/files/185/=charmm2gromacs-pvm.py
which claimed could convert the output from CGenFF into Gromacs format.
However, I tried many times and it always failed even with the advices
from previous thread. This
You don't. CGenFF is a forcefield, like CHARMM36. You install it, add rtp
entries then use pdb2gmx to generate a ligand's topology .itp file
On 2012-12-26 11:35:46AM +0100, Albert wrote:
hello:
I found the script charmm2gromacs-pvm.py
On 12/26/2012 12:18 PM, Peter C. Lai wrote:
You don't. CGenFF is a forcefield, like CHARMM36. You install it, add rtp
entries then use pdb2gmx to generate a ligand's topology .itp file
THX
but the problem is how to use this script? I've already download the
latest CGenFF file from CHARMM
Hi KT,
To update the number of atoms in a merged .gro file, assuming a single
frame and no empty lines after the box definition, you have to replace the
second line with the number of lines minus three:
sed '2s/^.*$/'$(wc -l file.gro)'/' file.gro out.gro
Cheers,
Tsjerk
On Tue, Dec 25, 2012
On 12/26/2012 12:39 PM, Peter C. Lai wrote:
It should come with two files. A .prm file, which contains the actual
forcefield parameters that you use the script to convert to bonded and
nonbonded .itp and atomtypes.atp The .rtf file is the charmm equivalent of
our .rtp file: it contains some
Dear justin
Thank you for your Previous reply
I Have Successfully constructed topology for cyclic peptide using spce bond
and Other Appropriate Changes in the . top files
Yet I Want to make CO Terminal But When I interactively Choose the Terminal
By pdb2gmx It Shows Only
On 12/26/12 9:50 AM, vidhya sankar wrote:
Dear justin
Thank you for your Previous reply
I Have Successfully constructed topology for cyclic peptide using spce bond
and Other Appropriate Changes in the . top files
Yet I Want to make CO Terminal But When I interactively
On 12/26/12 12:57 AM, Kavyashree M wrote:
Dear users,
I was using g_dih to find the phi/psi transitions of a protein
along the trajectory using the following command -
g_dih -f a.xtc -s a.tpr -o dihout.out -b x -e y -w
When it started running it indicated many of the following lines
Dihedral
Hi,
in vmd there is a package called topotools (
https://sites.google.com/site/akohlmey/software/topotools).
This package has the magic command writegmxtop.
Be carefull 'cause the created .top might miss some information (tipically
angles and dihedrals)
so I advice you to carefully check the .top
On 2012-12-26 13:00, Albert wrote:
On 12/26/2012 12:39 PM, Peter C. Lai wrote:
It should come with two files. A .prm file, which contains the actual
forcefield parameters that you use the script to convert to bonded and
nonbonded .itp and atomtypes.atp The .rtf file is the charmm
equivalent of
On 12/26/2012 07:53 PM, David van der Spoel wrote:
Hey, it's open source. Let us know how it goes
you can simple create an account and login
https://www.paramchem.org/
after your login, click upload molecule in left panel. Now you will
see the option:
Include parameters that are already
Unfortunately, g_dih was written before 1997 and its documentation is very
poor. It does not actually read the connectivity in the .tpr file, nor does
it attempt to infer connectivity other than for some protein backbone
dihedrals. For some reason, it thinks it finds some for your topology, but
On 2012-12-26 20:29, Albert wrote:
On 12/26/2012 07:53 PM, David van der Spoel wrote:
Hey, it's open source. Let us know how it goes
Sorry what I meant was: If you make a better version of the
charmm2gromacs script, then please upload it to the website.
Cheers, David.
you can simple
Hi everybody,
Im trying to use GROMACS for MD of a RNA model generated by Rosetta
(FARFAR). As a test I try processing a modelledpdb file. When I prepare
thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh
) from pdb I encounter following output :
Sorting it all out...
Opening force
Thank Francesco :-)
On Wed, Dec 26, 2012 at 11:31 PM, francesco oteri francesco.ot...@gmail.com
wrote:
Hi,
in vmd there is a package called topotools (
https://sites.google.com/site/akohlmey/software/topotools).
This package has the magic command writegmxtop.
Be carefull 'cause the
Do you mean that i have to add the line sed '2s/^.*$/'$(wc -l file.gro)'/'
file.gro out.gro into the old script merge.py ?
On Wed, Dec 26, 2012 at 6:39 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi KT,
To update the number of atoms in a merged .gro file, assuming a single
frame and no
On 12/26/12 6:32 PM, Gert Peters wrote:
Hi everybody,
Im trying to use GROMACS for MD of a RNA model generated by Rosetta (FARFAR).
As a test I try processing a modelledpdb file. When I prepare thetopology
files (pdb2gmx -f test.pdb -ff amber99 -ignh ) from pdb I encounter following
output :
On 12/26/12 7:46 PM, Kieu Thu Nguyen wrote:
Do you mean that i have to add the line sed '2s/^.*$/'$(wc -l file.gro)'/'
file.gro out.gro into the old script merge.py ?
sed is a standard *nix command, issued from the command line.
-Justin
On Wed, Dec 26, 2012 at 6:39 PM, Tsjerk Wassenaar
On Thu, Dec 27, 2012 at 12:32 AM, Gert Peters gert.pet...@ugent.be wrote:
Hi everybody,
Im trying to use GROMACS for MD of a RNA model generated by Rosetta
(FARFAR). As a test I try processing a modelledpdb file. When I prepare
thetopology files (pdb2gmx -f test.pdb -ff amber99 -ignh
) from
Thanks both of you for the suggestions.
Regarding the backup files - I did not run the command
multiple times.
Thank you
kavya
On Thu, Dec 27, 2012 at 1:01 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
Unfortunately, g_dih was written before 1997 and its documentation is very
poor. It does
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