Hi,
If you want to obtain coordinates for a small compound and have a smiles
description of the molecule (or an sdf file) I suggest Frog:
http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog
Miguel
2008/6/17 huan [EMAIL PROTECTED]:
Hi gmx users and developers.
I am wonder is there any other
huan wrote:
Hi gmx users and developers.
I am wonder is there any other program or server which
can use to obtain a pdb file? Currently i am using the
Dundee Pro Drg Server. I am looking for other program
or server.
There's an option or two here
If you include in the .itp file all the necessary combinations in those
sections, then yes, the .itp file is reasonable and will use the OPLS-AA
parameters for those specified items. Take care to get the numbering
right after that point, because you will likely be inserting lots of
hydrogens!
Vitaly Chaban wrote:
I've got a discrepancy calculating the diffusion coefficient via
Green-Kubo equation and via Einstein equation.
$ g_velacc -nonormalize -acflen 1001
$ g_analyze -f vac.xvg -integrate
Do I miss any important keyword here? It seems the result of integration is
Dear all,
RMSD and RMSF of my protein is showing abnormal flucutuation. To
overcome this problem I am using following commands--
trjconv -f *.trr -o trajout_whole.xtc -s *.tpr -pbc whole
trjconv -f trajout_whole.xtc -o trajout_nojump .xtc -pbc nojump
can i put the partial charges from Gaussian?
--- On Tue, 17/6/08, Justin A. Lemkul [EMAIL PROTECTED] wrote:
From: Justin A. Lemkul [EMAIL PROTECTED]
Subject: Re: [gmx-users] gromos parameterisation in OPLS
To: [EMAIL PROTECTED], Gromacs Users' List gmx-users@gromacs.org
Date: Tuesday, 17
Florian Dommert wrote:
Vitaly Chaban wrote:
I've got a discrepancy calculating the diffusion coefficient via
Green-Kubo equation and via Einstein equation.
$ g_velacc -nonormalize -acflen 1001
$ g_analyze -f vac.xvg -integrate
Do I miss any important keyword
On Tue, 17 Jun 2008 17:31:53 +0530 (IST)
ANINDITA GAYEN [EMAIL PROTECTED] wrote:
can i put the partial charges from Gaussian?
In principle you can do everything assuming that it is justified.
Putting charges from Gaussian do not mean much. It sounds very elaborated
because Gaussian could
I thought the flag -mol
calculates
the momentum autocorrelation function, so in my opinion the result has
to be divided
by the square of the masses of the molecules to obtain the diffusion
constant.
Flo, you're completely right. Sorry for my mistake as for
normalization here.
--
Vitaly
On Tue, Jun 17, 2008 at 02:21:09PM +0200, Xavier Periole wrote:
On Tue, 17 Jun 2008 17:31:53 +0530 (IST)
ANINDITA GAYEN [EMAIL PROTECTED] wrote:
can i put the partial charges from Gaussian?
In principle you can do everything assuming that it is justified.
Putting charges from Gaussian
Anamika Awasthi wrote:
Dear all,
RMSD and RMSF of my protein is showing abnormal
flucutuation. To overcome this problem I am using following commands--
trjconv -f *.trr -o trajout_whole.xtc -s *.tpr -pbc whole
trjconv -f trajout_whole.xtc -o trajout_nojump
Dear All,
My protein is simulating for 20 ns and 16 ns has already over, but I
want to analyze RMSD and RMSF for this 16 ns simulation, without stopping
the running simulation.it was crashed before, so I used tpbconv -f
previous.trr -e previous.edr -s previous.tpr -o new.tpr -until 2
Check your input/output!
In this case it seems you are missing/forgetting the -s flag to
specify the name of the tpr-file.
/Per
17 jun 2008 kl. 17.07 skrev Anamika Awasthi:
Dear All,
My protein is simulating for 20 ns and 16 ns has already
over, but I want to analyze RMSD
I would also suggest to use the xtc and not the trr file for analysis.
The (compressed) xtc is usually written more often than the
(full-precision) trr.
Jochen
Anamika Awasthi wrote:
Dear All,
My protein is simulating for 20 ns and 16 ns has already over,
but I want to analyze
Check the real posres(... routine in src/gmxlib/bondfree.c
Jochen
Jae Hyun Park wrote:
Dear GROMACS users,
I would like to modify the source code on the position restraint part
(restraining the atoms in a protein using -DPOSRES). Could anybody let me know
where (or which subroutine) I can
Dear All,
Please tell, what should I predict from this graph?
I can understand this is normal type of graph.
Sorry for inconvenience, but I want to ask some questions,
my this job crashed many time, because of power shut down and I had to
restart this again and again, I used
Jochen Hub wrote:
I would also suggest to use the xtc and not the trr file for analysis.
The (compressed) xtc is usually written more often than the
(full-precision) trr.
Well, if the user set it up that way. If they have done so, they they
should be able to remember which is better for
Anamika Awasthi wrote:
Dear All,
Please tell, what should I predict from this graph?
We can't tell from your graph what's happening because you haven't told
us how you generated it. It's also not our job to do so - it's yours.
You can go at look at your data at the points that have
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