Hi,
In .rtp file of a GROMOS 96 force field (ffG43a1.rtp for example),
exclusions seem to be listed only for aromatic residues such as TYR, HIS,
and TRP.
Why is that so?
Sanghwa Han
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Dear Gromacs users,
I have successfully installed Amber FF in Gromacs according to the
instruction by the Pande Group (http://folding.stanford.edu/ffamber/).
I ran a demo successfully and enjoyed the speed of Gromacs.
My questions are:
[Question 1] The topology file produced by pdb2gmx with
: Tuesday, June 19, 2007 4:31 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Format of a Topology File When Using Amber FF
inGromacs
한상화 wrote:
Dear Gromacs users,
I have successfully installed Amber FF in Gromacs according to the
instruction by the Pande Group (http
Dear GROMACS users,
I am trying to run md of a protein with a non-standard residue.
It was fine up until I ran mdrun with pr.mdp, where I received a LINCS
warning after 20 steps (0.042 ps).
Step 21, time 0.042 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max
Dear all,
Is there any way to make a disulfide between protein CysSH and GSH? Or an
interchain disulfide?
I am interested in running MD for Protein-S-SG (i.e. glutathiolated
protein).
Thanks
Sanghwa Han
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gmx-users mailing list
or flag for this
purpose).
Thanks
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Mark Abraham
Sent: Wednesday, January 17, 2007 2:19 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Disulfide between protein Cys and GSH
한상화 wrote:
Dear
for intermolecular disulfide.
Sanghwa han
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Mark Abraham
Sent: Wednesday, January 17, 2007 3:09 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Disulfide between protein Cys and GSH
한상화 wrote
Subject: Re: [gmx-users] Disulfide between protein Cys and GSH
한상화 wrote:
Thank you Mark.
The method you suggest is exactly what I tried.
I prepared a structure of two molecules in which the S...S distance was
made to be 0.206 nm (this value is within the tolerance).
But when I ran pdb2gmx
Dear gromacs users,
I am running MD for a protein with 212 amino acid residues.
When I run grompp (grompp -f pn_md.mdp -c pn_md.pdb -r pn_md.pdb -p pn.top -
o pn_md.tpr ) for the final product MD, I receive the following error
message.
I properly included sol and ion in the temperature
Dear Gromacs users,
I have gone through all the way to the final product MD, where I received
the following error message for grompp.
The same topology file pn.top did not give me any problem in the previous
steps including grompp with pr.mdp or grompp with em.mdp.
I included solvent and
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