On 6/14/2007 1:14 AM, Erik Lindahl wrote:
Hi Robert,
On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote:
These are all fine points. However, the question I'm asking is why do
Gromacs tools change atoms named OXT in PDB files to O2? Of course
there are always workarounds i.e. just simply change the atom name in
the coordinate file. However, I was wondering if anyone knew why this
happened. I suppose I will submit a bugzilla.
Don't bother for now :-)
This is because of a few old brain-dead choices in pdb2gmx, but we're
working on replacing that completely, and then we'll be name-agnostic.
The only thing I can say in our defense is that most other programs
also push their own naming convention when generation hydrogens, etc.
For instance, charmm will rename the resname of the first/last few
atoms in each chain to NTER/CTER.
Hi, Robert
I am clueless why this topic has again made people upset about Gromacs.
You may search for "David Mathog" in mailing list archive.
e.g. http://www.gromacs.org/pipermail/gmx-users/2006-February/020087.html
David, in the end, contributed some conversion script you might take a look.
I admit that it is frustrated to add on more rules when I want to let
pdb2gmx pass my PDB file. But when you are working with different force
field, AMBER, CHARMM and OPLS-AA, like me, pdb2gmx will definitely have
a dilemma to choose which atom instead of a fixed answer. Since, as you
say, it is easy to change the atom name, why don't you do yourself?
IMHO, it is rather to have a strict program which is faithful and rigid
than to have an "smart" one which may induce errors. Of course, I
believe Erik has a better idea to solve this problem.
Cheers,
Erik
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