[gmx-users] invalid order of directive moleule type

Anton Feenstra feenstra at few.vu.nl
Tue Nov 7 12:47:01 CET 2006

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!



  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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 |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |

More information about the gromacs.org_gmx-users mailing list