Hi Justin,
Thank you for your descriptive reply.
I prepared new index.file which includes mainchain, and when I used the
do_dssp with -n index.ndx, it worked.
But, if I doesn't use the index file, again, the Protein is selected by
the system. It is weird..
Best regards,
Deniz
On Thu, Jun 7,
Hi Mark,
Thank you for your reply.
Let me explain the problem a little more and answer your questions. I would
be happy if you could expound upon your reply.
Hi Gromacs users,
I created a lipopeptide (lauroic acid connected to an 8-residue peptide
which starts with Valine).
How
Hi Gromacs users,
I created a lipopeptide (lauroic acid connected to an 8-residue peptide
which starts with Valine).
· If I try to use pdb2gmx with -ter flag (Start terminus VAL-2:
None, End terminus ASP-9: COO-), everything seems to work (topology is
created.).
· But, if I
Hi all,
I wrote a own code to put three identical lipopeptide at desired positions.
Then I used the pdb2gmx with –ter flag to get the system’s topology, I have
encountered the following error:
Fatal error:
Atom OXT in residue ASP 18 was not found in rtp entry ASP with 9 atoms
while sorting
Hi Gromacs users,
We would like to apply strain to the system. Is this possible to do with
gromacs and if it is how?
Thank you in advance,
Deniz
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Hi gromacs users,
I wish to simulate a system using the Gromos53a6 force field. When I try to
run, I get the following errors:
ERROR 1 [file topol.top, line 194]: No default LJ-14 types
ERROR 2 [file topol.top, line 195]: No default LJ-14 types
ERROR 3 [file topol.top, line 198]: No
mark.abra...@anu.edu.auwrote:
On 12/04/2011 10:30 PM, Emine Deniz Tekin wrote:
Hi Mark,
Thank you for your reply. But, I couldn’t understand very well what you
meant “you can make one that uses backbone-style linking. Most of the
forcefields will have examples of non-amino-acid terminating
mark.abra...@anu.edu.auwrote:
On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote:
Hi Gromacs users,
I want to covalently link the lauroic acid to the Valine residue (it is a
peptide (amide) bond), I know that I should update the specbond.dat.But
before updating this file, I need the NH as an N
Hi Gromacs users,
I want to covalently link the lauroic acid to the Valine residue (it is a
peptide (amide) bond), I know that I should update the specbond.dat. But
before updating this file, I need the NH as an N terminal of the first
residue (Valine). When I used pdb2gmx with the –ter flag,
it. Lecturing me on willingness is crossing
the line. How do you know how much I tried? Anyhow, thanks for your earlier
help, but you can simply skip my future postings.
Best regards,
Deniz
On Thu, Mar 17, 2011 at 12:00 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Emine Deniz Tekin wrote
On Fri, Mar 4, 2011 at 9:13 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 3/03/2011 11:42 PM, Justin A. Lemkul wrote:
bharat gupta wrote:
The residue is a chromophore of Green Fluorescent Protein. The parameter
file that I have got has the connection for serine and glycine :-
For
...@vt.edu wrote:
Emine Deniz Tekin wrote:
Hi gromacs users,
I am using the gromacs 4.5.3 version. I created a lipopetide which consist
of 12 Carbon atoms (tail) connected to Val-Val-Ala-Gly-Glu-Arg-Gly-Asp
(residues) using ARGUSLAB and I saved it as a pdb file.
Then, when I used
Hi gromacs users,
I am using the gromacs 4.5.3 version. I created a lipopetide which consist
of 12 Carbon atoms (tail) connected to Val-Val-Ala-Gly-Glu-Arg-Gly-Asp
(residues) using ARGUSLAB and I saved it as a pdb file.
Then, when I used the following command in gromacs:
pdb2gmx –f
Hi Justin,
No matter what I search at gromacs search field, it gives the same error
message.
Deniz
On Wed, Feb 23, 2011 at 3:58 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Hi,
Is anyone else having problems using the search feature on the Gromacs
site? If I search for tutorials, I get:
14 matches
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