VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri May 22 2009 - 10:08:06 CDT

On Fri, 2009-05-22 at 10:19 -0400, Myunggi Yi wrote:
> This is very useful. Thanks.

if this is so useful, perhaps we should make it a plugin
that is bundled with VMD. i don't use amber, so i don't
know the translations required. if people would send those
to me, i could produce a generic version of this translator
(it could even be extended to other packages where a 1:1
mapping of naming conventions can be established).

there also is a script that would remove the bond between
the two hydrogen atoms, that amber uses for constraining,
which could be bundled in this plugin.

cheers,
   axel.

> BTW, if you have a correct .top file, then amber (tleap and ptraj)
> recognizes segments correctly without TER card.
>
>
> On Wed, May 20, 2009 at 5:28 PM, Axel Kohlmeyer
> <akohlmey_at_cmm.chem.upenn.edu> wrote:
> On Wed, 2009-05-20 at 15:49 -0400, Yi Shang wrote:
> > Dear there,
>
> dear miranda,
>
> > I wanted to load pdb files generated by VMD into tleap (in
> AMBER
> > package).
> > But I notice that Hydrogen naming in pdb files generated by
> VMD, is
> > different from those naming of pdb files generated by tleap.
> > for VMD pdbs: 2HD, 3HD, 2HG, HD21, HD32.....
> > for tleap pdbs: HD2, HD3, HG2, 1HD2, 2HD3......
> > It's giving my a hard time when I use ptraj (another program
> in AMBER
> > package)
> > and now tleap.
> >
> > I wonder how these naming inconsistency happened. And hope I
> can get
> > some suggestions here to get away with it.
>
>
> as far as i know, this has nothing to do with VMD itself, but
> rather
> the difference in naming conventions between charmm and amber.
> you can
> easily write a small script that converts between one and the
> other.
> it may be most convenient to put it into your .vmdrc
>
> say you create a list of mappings:
>
> set chm2ambmap = { {2HD HD2} {3HD HD3} {2HG HG2} {HD21 1HD2}
> {HD32
> 2HD3} ... }
>
> global chm2ambmap
>
> then you can do for the forward conversion:
>
> proc chm2amb {molid} {
> global chm2ambmap
>
> set cnt 0
> foreach p $amb2chm {
> set sel($cnt) [atomselect $molid "name [lindex $p 0]"]
> incr cnt
> }
>
> set cnt 0
> foreach p $amb2chm {
> $sel($cnt) set name [lindex $p 1]
> $sel($cnt) delete
> incr cnt
> }
> }
>
> and for the reverse process
>
> proc amb2chm {molid} {
> global chm2ambmap
>
> set cnt 0
> foreach p $amb2chm {
> set sel($cnt) [atomselect $molid "name [lindex $p 1]"]
> incr cnt
> }
>
> set cnt 0
> foreach p $amb2chm {
> $sel($cnt) set name [lindex $p 0]
> $sel($cnt) delete
> incr cnt
> }
> }
>
> and then just call the command
>
> chm2amb top
> or
> chm2amb 1
>
> whenever you want to convert a specific molecule's
> naming conventions. there are similar ones for the
> residue names, so you want to include this as well.
>
> > Another question: the VMD pdbs are single chain molecule by
> default,
> > how could I specify it to add 'TER' in between protein,
> ligand, or
> > water, water?
>
>
> right now you would have to write a small script that post
> processes your .pdb file with, e.g., awk, perl, or python,
> and split it apart based on some other information, e.g.
> segment name or chain id.
>
> making VMD insert these automatically would be conceivable
> if there was a consensus as to what indicator would be
> the correct one. there is, however, always the concern that
> any choice would break other programs that have different
> conventions.
> i would not want to have TER records between individual
> waters,
> though, as that would blow files up significantly.
>
> cheers,
> axel.
>
> >
> > Thank you all!
> >
> >
> >
> > --
> > Miranda
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of
> Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a
> better idiot.
>
>
>
>
> --
> Best wishes,
>
> Myunggi Yi
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
>
> http://sites.google.com/site/myunggi/
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.