[gmx-developers] development

Luke Czapla czapla at rutchem.rutgers.edu
Fri Nov 29 08:37:04 CET 2002


  I have created an updated version of pdb2gmx which corrects a very
minor bug and implements the proper reading of PDB files from the nucleic
acid database.

I was wondering if I could upload them via CVS since I don't have a user
name or password.  The changes are only 1 line for the bug - pdb2gmx
doesn't recognize 1 letter residues such as F, and it is in resall.c).
Also I added about 15 lines to read residue names in the form A T G C in
the PDB files (from the NDB) through pdb2gmx and use the normal internal
DADE ADE DGUA GUA and so on for DNA or RNA without having to touch the rtp
file.  Modifying the hydrogen database (hdb file) is still necessary,
however, unless someone could suggest a workaround for that.  I also am
working on fixing the 5'-end base to eliminate the missing phosphate
warnings.  Maybe someone has an idea for that too.

I sent this email to both gromacs lists, since this is my first time
posting on developers and it relates to some information I was pursuing on
users. The way I implemented the new DNA/RNA pdb2gmx method was for each A
T G or C encountered in the PDB file, I look for a corresponding ribose
O2* to determine whether it is RNA or not.


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