[gmx-developers] Re: [gmx-users] development

Erik Lindahl lindahl at stanford.edu
Fri Nov 29 20:23:54 CET 2002

Hi Luke,

The easiest way is to produce a diff file with

diff -aur <original_file> <new_file>

Where <original_file> is a recent version from CVS (I don't think we've 
changed pdb2gmx much lately, though).

Just post it and I'll apply it immediately. I'm sure we can arrange for 
CVS write access too if you plan to fix more things!



Luke Czapla wrote:

>  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.
>gmx-users mailing list
>gmx-users at gromacs.org
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