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 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
