Dear all,
I want to install Extended Genbox from gerrit.
https://gerrit.gromacs.org/#/c/1175/
How can I put this code into my existing gromacs installation?
Thanks.
Regards,
Tegar
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please s
I was pretty confident that I am modifying the right file. apparently I did not
access to the main file; so I asked my supervisor and he provided me with a
proper access to the files.
Thanks again Justin.
- Original Message -
From: "Justin Lemkul"
To: "Discussion list for GROMACS users
Many thanks Justin.
Apparently I was modifying the .rtp file in the wrong location; now the pdb2gmx
works and I can start the modelling.
I also have some concern about my pdb file. i generated from my drawing in
Avogadro, with some arbitrary bond length and angle. I hope that I can find
the c
On 9/30/13 4:40 PM, Ehsan Sadeghi wrote:
Many thanks Justin.
Apparently I was modifying the .rtp file in the wrong location; now the pdb2gmx
works and I can start the modelling.
In the future, make sure you're providing accurate answers to the questions
being asked. I asked about this at
One a system passes EM and a couple of ps of MD, is it always stable
indefinitely? If not, then
something is wrong somewhere.
-- original message --
Dear Chris,
I put one tip5p molecule in a center of dodecahedral box - 2nm from that
molecule to walls, filled it with tip5p, ran 6000 steps of st
On 9/30/13 2:23 PM, Ehsan Sadeghi wrote:
Yes, I have introduced the new .rtp entry in
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp.
What could be wrong?
The outcome defies logic. If the .rtp entry were in that file, pdb2gmx would
not throw that error. Can you provide
Yes, I have introduced the new .rtp entry in
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.rtp.
What could be wrong?
- Original Message -
From: "Justin Lemkul"
To: "Discussion list for GROMACS users"
Sent: Monday, September 30, 2013 11:16:57 AM
Subject: Re: [gmx-users]
On 9/30/13 12:50 PM, Ehsan Sadeghi wrote:
Thanks Justin,
I modified the pdb file, but it cannot recognize my residue LIG. Here is the
error:
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading nafion5.pdb...
Read 46 atoms
Analyzing pdb file
Spl
Thanks Justin,
I modified the pdb file, but it cannot recognize my residue LIG. Here is the
error:
Opening force field file
/usr/local/gromacs/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading nafion5.pdb...
Read 46 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or
On 9/30/13 5:19 AM, suhani nagpal wrote:
Greetings
I have a large protein of 303 residues and one of the lysine is acetylated
in the same.
The forcefield selection according to the options says as follows:
Residue 'ALY' not found in residue topology database
For more information and tips for
Greetings
I have a large protein of 303 residues and one of the lysine is acetylated
in the same.
The forcefield selection according to the options says as follows:
Residue 'ALY' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
we
11 matches
Mail list logo