[gmx-users] CG to FG transformation error
Hi, I have successfully converted my CG (only) protein model to FG model using g_fg2cg command of the gromacs_reverse package. But now when I try to compile my .mdp file for SA run, grompp is throwing some warnings: creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# WARNING 1 [file fg_protein.mdp, line unknown]: Unknown left-hand 'cap_force' in parameter file WARNING 2 [file fg_protein.mdp, line unknown]: Unknown left-hand 'cap_a' in parameter file WARNING 3 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restr' in parameter file WARNING 4 [file fg_protein.mdp, line unknown]: Unknown left-hand 'r_CGW' in parameter file WARNING 5 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restrW' in parameter file WARNING 6 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_steps' in parameter file WARNING 7 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_water' in parameter file checking input for internal consistency... calling /lib/cpp... processing topology... - My system contains only multiple copies of a protein. How to solve this issue? Any suggestion is welcome. Thanks, -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CG to FG transformation error
Anirban Ghosh wrote: Hi, I have successfully converted my CG (only) protein model to FG model using g_fg2cg command of the gromacs_reverse package. But now when I try to compile my .mdp file for SA run, grompp is throwing some warnings: creating statusfile for 1 node... Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# WARNING 1 [file fg_protein.mdp, line unknown]: Unknown left-hand 'cap_force' in parameter file WARNING 2 [file fg_protein.mdp, line unknown]: Unknown left-hand 'cap_a' in parameter file WARNING 3 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restr' in parameter file WARNING 4 [file fg_protein.mdp, line unknown]: Unknown left-hand 'r_CGW' in parameter file WARNING 5 [file fg_protein.mdp, line unknown]: Unknown left-hand 'fc_restrW' in parameter file WARNING 6 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_steps' in parameter file WARNING 7 [file fg_protein.mdp, line unknown]: Unknown left-hand 'rel_water' in parameter file checking input for internal consistency... calling /lib/cpp... processing topology... - My system contains only multiple copies of a protein. How to solve this issue? Any suggestion is welcome. Use proper .mdp settings. You're being told that your fg_protein.mdp contains numerous keywords that do not exist in normal Gromacs. -Justin Thanks, -Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CG to FG transformation error
Hi, I am trying to convert a coarse grained protein to a full atom model after CGMD. I am using the modified gromacs_reverse code available from MARTINI site. I am using the following command: g_fg2cg -pfg topol_fg.top -pcg pro_cg.top -n 0 -c pro_cg.gro -o full.gro But in the output full.gro all the atoms are having coordinate values as 0.00. My pro_cg.top file looks like: #define _FF_GROMOS96 #define _FF_GROMOS42A2 ;#define _FF_GROMACS ;#define _FF_GROMACS1 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 0.125 0.5 #include ffG43a2nb.itp #include ffG43a2bon.itp Is this correct? where I am going wrong? I think the problem is with pro_cg.top file only. Any suggestion is welcome. Thanks, -Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CG to FG transformation error
On 21 Jan 2011, at 14:47, Anirban Ghosh wrote: I am trying to convert a coarse grained protein to a full atom model after CGMD. I am using the modified gromacs_reverse code available from MARTINI site. I am using the following command: g_fg2cg -pfg topol_fg.top -pcg pro_cg.top -n 0 -c pro_cg.gro -o full.gro But in the output full.gro all the atoms are having coordinate values as 0.00. My pro_cg.top file looks like: #define _FF_GROMOS96 #define _FF_GROMOS42A2 ;#define _FF_GROMACS ;#define _FF_GROMACS1 [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 0.125 0.5 #include ffG43a2nb.itp #include ffG43a2bon.itp Is this correct? where I am going wrong? I think the problem is with pro_cg.top file only. No. The problem is indeed your pro_cg.top. It should be a *CG topology* (like what you've used for the CG simulations), not an *atomistic FF*. -martti- -- Post-doctoral research fellow Moleculaire Dynamica University of Groningen Nijenborgh 4, 9747AG Groningen, the Netherlands tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
