[gmx-users] if PRODRG calculate incorrectly

2011-09-17 Thread ahmet yıldırım
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

Re: [gmx-users] if PRODRG calculate incorrectly

2011-09-17 Thread Tsjerk Wassenaar
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

Re: [gmx-users] if PRODRG calculate incorrectly

2011-09-17 Thread Justin A. Lemkul
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

Re: [gmx-users] if PRODRG calculate incorrectly

2011-09-17 Thread ahmet yıldırım
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

Re: [gmx-users] if PRODRG calculate incorrectly

2011-09-17 Thread Mark Abraham
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 --

[gmx-users] Dimer simulation

2011-09-17 Thread Kavyashree M
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

[gmx-users] different sets of fudgeQQ and fudgeLJ

2011-09-17 Thread Yun Shi
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

Re: [gmx-users] different sets of fudgeQQ and fudgeLJ

2011-09-17 Thread Mark Abraham
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