Hi Harpreet, Regarding the message "invalid order ...", check the archives of this mailing list. Further note that you shouldn't use the gmx (ffgmx) force field, but should choose one of the Gromos force fields (united atom), OPLS or Encad (all-atom).
Specific to your problem is that there is a mismatch between the names of atoms in the .pdb file and the names in the residue database (.rtp) file of the force field you chose. Usually, it's best to modify the names in the .pdb file to match those in the .rtp file. By the way, since you're new to Gromacs.., have you tried the MD/Gromacs tutorial from the MD group in Groningen? If not, it may be a good start to get to know gromacs. At present the Groningen group is off the air, but I've mirrored the site at: http://nmr.chem.uu.nl/~tsjerk/MDCourse/ Hope it helps, Tsjerk On 11/7/06, merc mertens <[EMAIL PROTECTED]> wrote:
if i were you, i would rather adapt my pdb file to an existing forcefield as ffgmx, than trying to generate a new forcefield that fits to your pdb with prodrug. the first option seems much easier to me. what i mean is, if you change the names of you FAD atoms to the ones you see in the *rtp they will be recognized by pdb2gmx. -------- Original-Nachricht -------- Datum: Tue, 07 Nov 2006 11:35:47 +0000 Von: "harpreet singh" <[EMAIL PROTECTED]> An: gmx-users@gromacs.org Betreff: [gmx-users] invalid order of directive moleule type > Hi All, > I am new to this package and want your help. I am trying to use GROMACS to > study energy minimization and molecular dynamics for FAD molecule. I am > having the following problems. > 1. I tried to run pdb2gmx for PDB file for FAD downloaded from > http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl site. and used the > gromacs force field . The program gave the following error: - > Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.hdb > Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx-n.tdb > Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx-c.tdb > > Back Off! I just backed up fad_test.top to ./#fad_test.top.1# > Processing chain 1 (53 atoms, 1 residues) > There are 0 donors and 0 acceptors > There are 0 hydrogen bonds > ------------------------------------------------------- > Program pdb2gmx, VERSION 3.3.1 > Source code file: pdb2gmx.c, line: 393 > Fatal error: > Atom O1P in residue FAD 1 not found in rtp entry with 61 atoms > while sorting atoms > On comparing topology file (ffgmx.rtp) for FAD entry i was surpried to see > that it has atom type enteries OP1, OP2 instead of O1P, O2P in downloaded > PDB file (fad.pdb). Also atom type at number 23 was O in ffgmx.rtp (for > FAD) and O3P was missing in this file. I am attaching the files herewith. > > 2. I tried to make .top and .gro files (fad92.top and fad.gro > respectively) > ,using PRODRG2 server. and used them with grompp commad > > grompp -f em.mdp -c fad92.gro -p fad92.top -o fad92.tpr > > This resulted in the following error. > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7# > checking input for internal consistency... > calling /usr/bin/cpp... > processing topology... > Cleaning up temporary file gromppfYcUxi > ------------------------------------------------------- > Program grompp, VERSION 3.3.1 > Source code file: topio.c, line: 388 > > Fatal error: > Invalid order for directive moleculetype, file ""fad92.top"", line 15 > ------------------------------------------------------- > > "Oh, There Goes Gravity" (Eminem) > > Kindly guide me to solve this problem. > Thanks in advance > > Harpreet Singh > > _________________________________________________________________ > Use your PC to make calls at very low rates > https://voiceoam.pcs.v2s.live.com/partnerredirect.aspx > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 -- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
-- Tsjerk A. Wassenaar, Ph.D. post-doc NMR, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
