://www.ks.uiuc.edu/Research/vmd/plugins/molfile/ and try
some
alternatives.
Mark
On Fri, Oct 18, 2013 at 2:10 PM, anu chandra anu80...@gmail.com wrote:
Hi Mark,
Yes. I do can able to load the trajectories successfully in VMD with the
file format option of ' AMBER coordinate
can not able to read latest ones.
On Sat, Oct 26, 2013 at 12:21 PM, anu chandra anu80...@gmail.com wrote:
Hi,
Sorry for the late reply. I have tried all the possibilities with filename
extension as mentioned in the VMD molfile details. As said, VMD uses .crd
or .crdbox filename extensions
itself?
Mark
On Oct 18, 2013 6:21 AM, anu chandra anu80...@gmail.com wrote:
Dear Gromacs users,
I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing
few
analysis. Unfortunately I ended-up with the following error
Dear Gromacs users,
I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing few
analysis. Unfortunately I ended-up with the following error.
GROMACS will now assume it to be a trajectory and will try to open it using
Thanks a lot for reply.
On Mon, Oct 14, 2013 at 12:34 PM, bipin singh bipinel...@gmail.com wrote:
g_mindist with -on and -d option.
On Mon, Oct 14, 2013 at 11:37 AM, anu chandra anu80...@gmail.com wrote:
Dear Gromacs users,
I am working with protein-ligand interaction. I would like
Dear Gromacs users,
I am working with protein-ligand interaction. I would like to calculate the
number of contacts ligand make with the protein within a specific cut off (
say within 3.5 to 4.5 angstroms), along the simulation trajectories. Is
there any Gromacs analysis script, which can help me
and regards
Anu
On Thu, Apr 11, 2013 at 9:05 PM, David van der Spoel
sp...@xray.bmc.uu.sewrote:
On 2013-04-10 08:33, anu chandra wrote:
Dear Gromacs users,
I would like to do side-chain dihedral angle PCA for my protein. The
protein contains 293 residues. I came across an explanation about
Dear Gromacs users,
I would like to do side-chain dihedral angle PCA for my protein. The
protein contains 293 residues. I came across an explanation about dihedral
PCA in gromcas website (
http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA). Is it possible
to do side-chain dihedral PCA
:28 PM, Justin Lemkul jalem...@vt.edu wrote:
On Mon, Apr 1, 2013 at 4:52 AM, anu chandra anu80...@gmail.com wrote:
Dear amber users,
I am working with protein-ligand interaction. The protein shows high
degree
of side-chain conformational changes and minimal backbone conformational
Dear amber users,
I am working with protein-ligand interaction. The protein shows high degree
of side-chain conformational changes and minimal backbone conformational
changes during ligand binding. In order to capture these side chain
flexibility, as a initial step, I would like to do clustering
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