Re: vmd-l: merging two pdb files

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Thu Nov 08 2007 - 09:29:54 CST

Hi Dibyadeep,

Concatenating multiple pdb files is the first (important step). If you
want your 2 proteins to be 2 different segments, you would need a
'TER' separating them. Also, you can write little scripts where you
renumber your atom index, resid and segid to have what you desire. I
don't think there is any standardized code to do this..you have to get
down to writing scripts for what you want!

This is an example, where I renumber my water molecules at the end of
my protein:

#load the system
set sys [mol new cat1.pdb]
# make atomselections
set all [atomselect $sys all]
set solv [atomselect $sys "segname WAT"]
# Renumber resids
set numSolv [expr {[$solv num]/3}]
# Assuming the last resid of my protein is 450
set beg 450
set residlist {}
for {set i 1} {$i<=$numSolv} {incr i} {
        for {set j 0} {$j<3} {incr j} {
                set resid [expr {$beg + $i}]
                lappend residlist $resid
        }
}
$solv set resid $residlist
# Write out the nice new pdb file
$all writepdb new_cat.pdb

 This is just a pointer to what you might do... Hope this help!

Best,
Neelanjana

On Nov 8, 2007 6:24 AM, Dibyadeep Paul <dibyadeep_at_gmail.com> wrote:
> Sir, will just merging together two pdb files that work? What I want
> is to have another pdb file, which will be have the two protein
> molecules simultaneously, so that I can directly use the single file,
> instead of the two files. Wont it also be necessary to modify the
> numbering of the atoms and molecules etc? I dont think these can be
> achieved by simply using cat.
>
> Sincerely
>
> Dibyadeep
>
> On Nov 8, 2007 6:09 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
> > On Thu, 8 Nov 2007, Dibyadeep Paul wrote:
> >
> > DP> Hii all
> > DP>
> > DP> I am actually a new user of vmd. Is there any way to merge together
> > DP> two pdb files using vmd? Although I tried a lot, I couldn't do so. If
> > DP> not what program would you use to do so.
> >
> > you could use the extremely sophisticated program 'cat'
> > to merge those files (it was written solely for the
> > purpose of concatenating files). for more details try
> > cat --help (it helps if you do this on a linux machine...).
> >
> > <g>,
> > axel.
> >
> > DP>
> > DP> Sincerely
> > DP>
> > DP> Dibyadeep
> > DP>
> >
> > --
> > =======================================================================
> > 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.
> >
>

-- 
****************************************
Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
USA
Phone: 1-949-824 9921
email: sengupta_at_uci.edu
****************************************

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