Dear Dr. Xavier Periole, Thank you for guiding me through. I could solve the problem of setting up the system for minimization. However When started minimization run for 2000 steps with steepest descent , I encountered yet another problem. which is as follows .. Started Steepest Descents on node 0 Tue Dec 11 17:48:57 2007 Removing pbc first time Done rmpbc Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 2000 Grid: 4 x 5 x 4 cells calc_bor: cg0=0, cg1=553, ncg=553 CG0[0]=0, CG1[0]=553 CG0[1]=0, CG1[1]=0 calc_bor: cg0=0, cg1=553, ncg=553 CG0[0]=0, CG1[0]=553 CG0[1]=0, CG1[1]=0 Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. Step Time Lambda 0 0.00000 0.00000 calc_bor: cg0=0, cg1=553, ncg=553 CG0[0]=0, CG1[0]=553 CG0[1]=0, CG1[1]=0 ------------------------------------------------------- Program mdrun, VERSION 3.3 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 80 ] Please report this to the mailing list (gmx-users@gromacs.org) ------------------------------------------------------- Now where do I go from here? Its asking me to energy minimize the system which what I am trying to do ! What is this ci value and why is it so high? Kindly help me I am once again stuck. regards sharada -- Original Message -- From: "Xavier Periole" <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Date: Tue, 11 Dec 2007 12:07:27 +0100 Subject: Re: Fw: Re: [gmx-users] Methanol SOL :Number of solvent molecules = 0 in your agg2t.top you should replace the last line : SOL XXX by: Methanol XXX which is the name of the molecule. You should also remove the angle definition in methanol.itp. Placing a ";" at the beginning of the line is enough. XAvier On Tue, 11 Dec 2007 15:40:04 +0530 (IST) sharada <[EMAIL PROTECTED]> wrote: > > > > > > > > > > > > > > > > > > > > Dear Mark Abraham, > I have changed MeoH to SOL in .gro and .itp files and also changed the >#include line to "methanol.itp" > It now seemed to have written the solvent molecules in the top file with SOL >as the name with atom types of methanol. > When I ran grompp program as following I get the error as shown below: I am >also attaching the .gro,.itp,.top files. for information. Did I miss out >anything ? > grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr > [EMAIL PROTECTED] Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top > -o >agg2_em.tpr > > Option Type Value Description > ------------------------------------------------------ > -[no]h bool no Print help info and quit > -[no]X bool no Use dialog box GUI to edit command line options > -nice int 0 Set the nicelevel > -[no]v bool yes Be loud and noisy > -time real -1 Take frame at or first after this time. > -np int 1 Generate statusfile for # nodes > -[no]shuffle bool no Shuffle molecules over nodes > -[no]sort bool no Sort molecules according to X coordinate > creating statusfile for 1 node... > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7# > checking input for internal consistency... > calling /lib/cpp... > processing topology... > Generated 141 of the 1176 non-bonded parameter combinations > Excluding 3 bonded neighbours for Protein 1 > Cleaning up temporary file grompp5RBSRX > ------------------------------------------------------- > Program grompp, VERSION 3.3 > Source code file: toppush.c, line: 1264 >Fatal error: > No such moleculetype SOL > ------------------------------------------------------- > I never prefer working in root as I know the problems. Thanks for > suggesting. I needed to change the methanol.itp and methanol216.gro which >could be possible only through root. > regards > sharada > > > > > > > > > > > > ----------------------------------------------------- XAvier Periole - PhD NMR & Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole ----------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php