[gmx-users] the reson for neutralizing the charge

Hi I have a basic question about the charge. why is it important to neutralize the charge of ligand-protein complex. Is it true by neutralizing the tatal charge of ligand-protein complex we prevent the electrostatic intraction of ligand and protein? Any suggestion would be appreciated. --

[gmx-users] editconf 2 warning

Hi These 2 warning appeared after I did editconf for Drug-Protein Complex. WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type WARNING: vdwradii will be determined based on residue and atom names, this can

[gmx-users] partial charge on protein

Hi there is total charge of 0.08 on the protein, Is it correct to add 1 CL- or it should better ignore this? -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

[gmx-users] partial charge on protein

Hi according to my problem about non-neglible magnitude partial charge on protein, I did not use -missing option with pdb2gmx my command is: pdb2gmx -ignh -f .pdb -o .pdb -water spce what should I do to neutralize this charge? Thank you in advance. -- Tehran University of Medical Sciences

[gmx-users] partial charge on protein

Hi Justin and all when I do this command: pdb2gmx -ignh -f .pdb -o .pdb -water spce with OPLS force field. it seems that the protein has the charge of -3, while the ligand has the charge of 0.890 and finally it prints that the final charge is -2.11. I neutralized this charge with 2 NA+ so

[gmx-users] how to save grace out put to jpeg or grafifal pic

hi my ques. dose not exactly relate to the gromacs while it is about how I can save the resulting plot from grace in to the jpeg or other picture file. thanks -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by

[gmx-users] how to save grace out put to jpeg or grafical pic

hi my ques. dose not exactly relate to the gromacs while it is about how I can save the resulting plot from grace in to the jpeg or other picture file. thanks -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by

[gmx-users] do_dssp fatal error

Hi thanks Dr. van der Spoel my previous problem fixed. I have another question. I download DSSP from http://swift.cmbi.ru.nl/gv/dssp/ from the part Distribution in the left partition of the page. it was the zip file and I unzip it and positioned it in my /usr/local/bin and adjust the .bashrc.

[gmx-users] (no subject)

Subject: Ion jump out of protein after MD Date: Sat, 14 Mar 2009 09:45:28 +0330 Message-Id: 20090314061153.m77...@razi.tums.ac.ir X-Mailer: OpenWebMail 2.53 20081220 334 X-OriginatingIP: 194.225.58.210 (hazizian) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Hi Sorry I

[gmx-users] ion jump out of protein

Hi I mean after MD the ion was not in the active site, the location of ion is out of the protein. My ion jump out of the protein after MD.My ion (MN) has not any covalant bond by its neibour, just has electrostatic intraction. is there any line that I have to add to the itp file or top

[gmx-users] how could have integrated structure after sa.

Hi 1- Is it possible to change the pbc condition from xyz(default) to no(vacume) after finishing the annealing, in order to reach an integrated sturcture instead of wraped one? 2- What command should I execute? is fixed by trjconv? 3-It is probably a simple question, in MD we have also PBC

[gmx-users] metal ion go out of protein after md

Hi after 30 ns MD, the 2 metal ion (MN) jumpe out of their active site, why does it ocure? how could I fix this problem, is it necessary to do the job again? Thank's for replying. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and

[gmx-users] metal ion go out of protein after md

Hi MN in my active site participate in electrostatic intraction. I did not define any covalant bonds in topology file. What should I do in the case of Electrostatic intraction? -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous

[gmx-users] do_dssp fatal error

Hi when I use do_dssp the following error come: Program do_dssp, VERSION 4.0.3 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro /dev/null 2 /dev/null How could I fix this. Thank you in advance. -- Tehran University of

[gmx-users] problem in pdb file after SA

Hi all I have done MD job on a 226 residue protein with cubic box -d 0.9 in the editconf step. after 30 ns I entered the last step pdb to the simulating annealing, again with cubic box and -d 0.9. the highest temp was 600 K and the loest was 50 K. When I see the pdb of structures at 300 K, 600

[gmx-users] vanishing trr file

Hi I have done gromacs simulating annealing but my trr file vanish. is there any ways to solve it. my job are now running but i can not see where it is saved. Thank you. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous

[gmx-users] Software inconsistency error.

Hi I want to have cg minimization after steep minimization of my MD result . but every time this error appeare. Program mdrun_mpi4, VERSION 4.0.2 Source code file: minimize.c, line: 404 Software inconsistency error: state mismatch in do_em_step What could be the reason ? Thanks. -- Tehran