[gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files
leafyoung at yahoo.com
Wed Jun 13 20:58:40 CEST 2007
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.
I am clueless why this topic has again made people upset about Gromacs.
You may search for "David Mathog" in mailing list archive.
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.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
> Please don't post (un)subscribe requests to the list. Use thewww
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
More information about the gromacs.org_gmx-users