[gmx-users] Problem in applying postion restrain on protein

Hello Justin sir sorry , The suggestion U given to me is not working. Actually I am a master student and just started to do simulation of membrane protein . Here no one did this work thats why i am facing more problem. sorry for putting question all the time in gmx-user list . But its only

[gmx-users] about estiminating the binding free energy by LIE method

Dear All: I would like to estimate the binding free energy between a drug molecule and its receptor. Inorder to do this, i run a MD simulation in which PME method was used to deal with long range electrostatic interaction. I need to calculate the VDW interaction energy and electorst

[gmx-users] estimate free energy bu LIE method, about long range electrostatic interaction

Dear All: I would like to estimate the binding free energy between a drug molecule and its receptor. Inorder to do this, i run a MD simulation in which PME method was used to deal with long range electrostatic interaction. I need to calculate the VDW interaction energy and electorsta

Re: [gmx-users] Re: Questions

Chih-Ying Lin wrote: Hi Tsjerk: I still have questions here. 1. Although you have explained the differece between HOH, AHOH and BHOH, I do not fully understand. => Can I delete all of atoms, HOH, AHOH and BHOH ? 2. So, in your tutorial, you use "united atom" algorithm, right? and, "pdb2gmx"

[gmx-users] Re: Questions

Hi Tsjerk: I still have questions here. 1. Although you have explained the differece between HOH, AHOH and BHOH, I do not fully understand. => Can I delete all of atoms, HOH, AHOH and BHOH ? 2. So, in your tutorial, you use "united atom" algorithm, right? and, "pdb2gmx" can recognize the "uni

Re: [gmx-users] what is meaning of vol 0.95 imb F 1%?

wuxiao wrote: > Dear gmx users, > If -v was passed on to mdrun, such rows one by one would be printed > continuously as follows: > vol 0.95 imb F 1% step 1000, will finish Thu Apr 30 15:39:33 > Obviously, the words "step 1000, will finish Thu Apr 30 15:39:33" mean > that the current running

[gmx-users] what is meaning of vol 0.95 imb F 1%?

Dear gmx users, If -v was passed on to mdrun, such rows one by one would be printed continuously as follows: vol 0.95 imb F 1% step 1000, will finish Thu Apr 30 15:39:33 Obviously, the words "step 1000, will finish Thu Apr 30 15:39:33" mean that the current running step is 1000, the whol

RE: [gmx-users] Error by pdb2gmx

Check consistency with other entries around it, easy way to check to see that you have the right format. What did you edit the file with? Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, P

Re: [gmx-users] Error by pdb2gmx

This is the new entry I added to the rtp file. [ PDM ] [ atoms ] SI SI 0.300 1 CH3opls_0690.000 1 O opls_108 -0.300 1 [ bonds ] SI O 0.190158805.0 SI CH3 0.164293160.0 [ dihedrals ] CH3SIO

Re: [gmx-users] Error by pdb2gmx

Yanmei Song wrote: Dear Justin and Dallas: Thank you for your help earlier. I made a copy of ffoplsaa.rtp to my working directory and add a new residue to it. Then perform the following command: pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp Opening library file /packages/groma

Re: [gmx-users] Error by pdb2gmx

Yanmei Song wrote: --- Program pdb2gmx, VERSION 3.3.3 Source code file: resall.c, line: 289 Fatal error: in .rtp file at line: --- Well that's not a terribly helpful error message, is i

Re: [gmx-users] Error by pdb2gmx

Dear Justin and Dallas: Thank you for your help earlier. I made a copy of ffoplsaa.rtp to my working directory and add a new residue to it. Then perform the following command: pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp Opening library file /packages/gromacs-3.3.3/share/gromac

[gmx-users] itp for rigid acetone

the parameter of acetone in the literature( JPC 94, 1990, p.1683) are given in the following manner, atom types charge sigma epsilon CH3 0.062 3.910 0.160 C0.300 3.750 0.105 O