[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. <> What could be the reason ? Thanks. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner,

[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 conte

[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] 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 o

[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 set

[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 dangerou

[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 c

[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 r

[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 f

[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 MailScan

[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 MailScan

[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. w

[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 d

[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 www.tu

[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 -0.11

[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. -- Teh