[gmx-users] pdb2gmx problems and modified AA's

[Anton Feenstra]

Dr Seth Carlton OLSEN wrote:

> Hi Gromacs Users,
> 
> Thanks David for that point.  I have renamed NE1 to NE3 (since there is also a CE2) in the rtp, hdb files and in the pdb I'm trying to process.  The fatal error then read:
> 
> Fatal error: Atom HE31 not found in rtp database in residue CRQ, it looks a bit like HE11
> 
> Accordingly, I changed the nitrogen-bonded hydrogen atoms (there should be 2) to HE31 and HE32 respectively.  However, this generated the following fatal errors:
> 
> WARNING: atom HD11 is missing in residue CRQ 62 in the pdb file
>          You might need to add atom HD11 to the hydrogen database of residue CRQ         in the file ff???.hdb (see the manual)

Did you also rename the atoms in the ffoplsaa.hdb?
The atom names must match exactly between .pdb (or .ent), .rtp and .hdb.
Atom names for the added H's are generated from the 'bonded' N or C, so
the H to CD1 will be HD11 and HD12.

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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