Dear users,
I have a problem related to PRODRG.
Chirality:NO
Full charges: YES
Energy minimization: NO
*İnput file name:TRS.pdb*
HETATM 1803 C TRS B 232 38.588 -4.733 65.956 1.00 17.99
C
ANISOU 1803 C TRS B 232 2126 1948 2760 -378 45-81
C
HETATM 1804 C1 TRS B
Hi Ahmet,
The PRODRG server is not related to Gromacs. If you encounter problems
pertaining to the server or the outcome from it, you should drop a
line to the PRODRG development team.
Cheers,
Tsjerk
2011/9/17 ahmet yıldırım ahmedo...@gmail.com:
Dear users,
I have a problem related to
ahmet yıldırım wrote:
Dear users,
I have a problem related to PRODRG.
Chirality:NO
Full charges: YES
Energy minimization: NO
_*İnput file name:TRS.pdb*_
HETATM 1803 C TRS B 232 38.588 -4.733 65.956 1.00
17.99 C
ANISOU 1803 C TRS B 232 2126 1948 2760 -378
Dear Tsjerk and Justin,
Thanks for your reply. I will contact the PRODRG developers.
can you suggest anyway/anytool for generating ligand coordinates/topologies?
Thanks in advance
17 Eylül 2011 15:58 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı:
ahmet yıldırım wrote:
Dear users,
I
On 17/09/2011 11:28 PM, ahmet yıldırım wrote:
Dear Tsjerk and Justin,
Thanks for your reply. I will contact the PRODRG developers.
can you suggest anyway/anytool for generating ligand
coordinates/topologies?
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
Mark
--
Dear users,
I was trying to simulate a protein dimer covalently bond with
a disulphide bond (230+230 aa long). I used usual protocol
as used for simulation of a monomeric protein, using gromacs-
4.5.3, dodecahedron box, tip4p water model and protein to
box distance of 1 (-d in editconf). In the
Hi all,
I want to apply different values of LJ and QQ scaling factors for two
interacting molecules A and B. Since I already have the .itp files for each
molecule, should I just add something like:
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
1
On 18/09/2011 8:58 AM, Yun Shi wrote:
Hi all,
I want to apply different values of LJ and QQ scaling factors for two
interacting molecules A and B. Since I already have the .itp files for
each molecule, should I just add something like:
[ defaults ]
; nbfunccomb-rule gen-pairs
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