RE: [gmx-users] invalid order of directive moleule type
Thanks for the valueable suggessions, but sir i am actually want to use this program for small molecules. I have taken single FAD molecule as u suggested modified the atom type as described in ffgmx.rtp, program results top and gro files using pdb2gmx, but while running grompp i am getting the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations WARNING 1 [file fad.top, line 128]: No default Bond types, using zeroes WARNING 2 [file fad.top, line 139]: No default Bond types, using zeroes WARNING 3 [file fad.top, line 141]: No default Bond types, using zeroes WARNING 4 [file fad.top, line 328]: No default Angle types, using zeroes WARNING 5 [file fad.top, line 329]: No default Angle types, using zeroes WARNING 6 [file fad.top, line 334]: No default Proper Dih. types, using zeroes WARNING 7 [file fad.top, line 336]: No default Proper Dih. types, using zeroes WARNING 8 [file fad.top, line 338]: No default Proper Dih. types, using zeroes WARNING 9 [file fad.top, line 341]: No default Proper Dih. types, using zeroes WARNING 10 [file fad.top, line 343]: No default Proper Dih. types, using zeroes Cleaning up temporary file gromppLLm3l8 --- Program grompp, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated --- I Need Love, Not Games (Iggy Pop Kate Pierson) Those errors mean exactly what they say, you have no definition (in the forcefield that you have used) for those bonds, angle and proper dihedral types. Moreover , suppose if we want to use this program (grompp) for say, a molecule which has no entry in any .rtp file provided with Gromacs and we grompp doesn't use the .rtp files, that is for pdb2gmx. use the PRODRG server, then how to deal with the error invalid molecular directive type. Amazing what you can find by searching the emailing list ;) http://www.gromacs.org/external/search.html http://www.gromacs.org/pipermail/gmx-users/2006-November/024540.html http://www.gromacs.org/pipermail/gmx-users/2003-December/008346.html Might be an idea to have a read through the manual as well, particularly the chapters on topologies. ___ gmx-users mailing listgmx-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
Re: [gmx-users] invalid order of directive moleule type
Thanks for the valueable suggessions, but sir i am actually want to use this program for small molecules. I have taken single FAD molecule as u suggested modified the atom type as described in ffgmx.rtp, program results top and gro files using pdb2gmx, but while running grompp i am getting the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations WARNING 1 [file fad.top, line 128]: No default Bond types, using zeroes WARNING 2 [file fad.top, line 139]: No default Bond types, using zeroes WARNING 3 [file fad.top, line 141]: No default Bond types, using zeroes WARNING 4 [file fad.top, line 328]: No default Angle types, using zeroes WARNING 5 [file fad.top, line 329]: No default Angle types, using zeroes WARNING 6 [file fad.top, line 334]: No default Proper Dih. types, using zeroes WARNING 7 [file fad.top, line 336]: No default Proper Dih. types, using zeroes WARNING 8 [file fad.top, line 338]: No default Proper Dih. types, using zeroes WARNING 9 [file fad.top, line 341]: No default Proper Dih. types, using zeroes WARNING 10 [file fad.top, line 343]: No default Proper Dih. types, using zeroes Cleaning up temporary file gromppLLm3l8 --- Program grompp, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated --- I Need Love, Not Games (Iggy Pop Kate Pierson) Moreover , suppose if we want to use this program (grompp) for say, a molecule which has no entry in any .rtp file provided with Gromacs and we use the PRODRG server, then how to deal with the error invalid molecular directive type. Kindly explain me regarding this error in detail, if you can spare some time for me. If you want i can give the sample files for what i am trying to do. Thanks From: merc mertens [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] invalid order of directive moleule type Date: Tue, 07 Nov 2006 13:00:02 +0100 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 + 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
Re: [gmx-users] invalid order of directive moleule type
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 + 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 listgmx-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 listgmx-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
Re: [gmx-users] invalid order of directive moleule type
harpreet singh wrote: 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. You cannot expect pdb2gmx to do magic. It needs a rational way of identifying what molecule you are trying to use. In order to do that, it will match, first, residue name (from pdb) to building block (in rtp). Second, it will match atom names using some tricks to account for common variations in names, because one cannot assume a defined order of the atoms within a residue/molecule/building block. If pdb2gmx fails to match atom names, you will have to help it by (manuall) matching the atoms in your pdb file with those in the rtp. According to your taste, you can either rename atoms in the pdb (to match the rtp), or make a new building block in the rtp and rename atoms there (to match the pdb, but be aware that building block names in the rtp must be unique *and* match the residue name in the pdb). Fatal error: Invalid order for directive moleculetype, file fad92.top, line 15 You probably didn't include the ffgmx.itp in your .top file (first, atomtypes, bondtypes etc. must be defined before you can define a moleculetype). Read the manual, please, especially those beautiful chapters on forcefields and on topologies! -- Groetjes, Anton _ ___ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 | | | [EMAIL PROTECTED] - www.few.vu.nl/~feenstra/ | | | If You See Me Getting High, Knock Me Down (RHCP)| |_|___| ___ gmx-users mailing listgmx-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
Re: [gmx-users] invalid order of directive moleule type
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 + 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 listgmx-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 listgmx-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 listgmx-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
