Hello guys:
I am building 11-cis-retinal topology these days. Here is what I did:
first of all, I build a small peptide like compound which
contains:11-cis-retinal connected to the protonated sidechain of LYS,
ACE and NME capped the N-term and C-term of the LYS respectively. With
this
Not directly. grompp does have the ability to pinpoint the current
line, but nobody has extended that to this part of the code. You can
hack in some crude output to src/kernel/topio.c and recompile if you
want some clues where the issue arises. Change line 647 of that file
to add the second line
On 07/06/2013 11:10 AM, Mark Abraham wrote:
set_warning_line(wi, cpp_cur_file(handle),
cpp_cur_linenr(handle));
warning_note(wi, Debugging);
Mark
Hello Mark:
thanks a lot for kind messages.
I changed above line in topio.c,
set_warning_line(wi,
My bad. Use
warning_note(wi, Debugging);
On Sat, Jul 6, 2013 at 11:39 AM, Albert mailmd2...@gmail.com wrote:
On 07/06/2013 11:10 AM, Mark Abraham wrote:
set_warning_line(wi, cpp_cur_file(handle),
cpp_cur_linenr(handle));
warning_note(wi, Debugging);
Mark
Hi Friends,
I am working on peptide self assembly.
I simulated two peptide which are random coil and apart from each other.
As the time process they start to interact and form antiparallel beta sheet
structure.
My plan is to find the energy difference in random coil to beta
shhet
On 07/06/2013 12:14 PM, Mark Abraham wrote:
My bad. Use
warning_note(wi, Debugging);
thanks a lot Mark. I've obtained some informations now:
Identified residue MET1 as a starting terminus.
Warning: Residue RETK296 in chain has different type (Other) from
starting residue MET1 (Protein).
Hi all gromacs users,
I have new forcefield and I have this folder in my working directory as well as
in /share/gromacs/top. When I run pdb2gmx from head node this forcefield
appears in list but when I run from slave nodes it do not appear in pdb2gmx
list. could somebody tell me how do
I think this question is for the developers of your operating system ...
Dr. Vitaly V. Chaban
On Sat, Jul 6, 2013 at 6:10 PM, Hari Pandey hariche...@yahoo.com wrote:
Hi all gromacs users,
I have new forcefield and I have this folder in my working directory as
well as in
On Sat, Jul 6, 2013 at 4:30 PM, Albert mailmd2...@gmail.com wrote:
On 07/06/2013 12:14 PM, Mark Abraham wrote:
My bad. Use
warning_note(wi, Debugging);
thanks a lot Mark. I've obtained some informations now:
That's a completely different output. I think both your executables
are broken,
This could be helpful, I hope.
http://www.gromacs.org/Documentation/File_Formats/FF.dat?highlight=change+ff+list
Dra.M.Florencia Martini
Cátedra de Farmacotecnia II
Facultad de Farmacia y Bioquímica
Universidad de Buenos Aires
Junín 956 6º (1113)
TE: 54 011 4964-8273
On 7/6/13 8:21 AM, rama david wrote:
Hi Friends,
I am working on peptide self assembly.
I simulated two peptide which are random coil and apart from each other.
As the time process they start to interact and form antiparallel beta sheet
structure.
My plan is to find the energy
On 7/6/13 4:17 PM, Mark Abraham wrote:
On Sat, Jul 6, 2013 at 4:30 PM, Albert mailmd2...@gmail.com wrote:
On 07/06/2013 12:14 PM, Mark Abraham wrote:
My bad. Use
warning_note(wi, Debugging);
thanks a lot Mark. I've obtained some informations now:
That's a completely different output.
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