VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Jun 03 2008 - 15:24:36 CDT

Sure, this is pretty straightforward to do with psfgen. You will
need 54 segment commands, each with a unique segname (and 54 coordpdb
commands). Then you will need to use the appropriate patches from
the topology file to connect things.

While it sounds like a lot, it could easily be done with a few loops,
i.e.,

for {set i 1} { $i < 19 } { incr $i} {

segment P$i {
pdb protein_$i.pdb
first ___
last ___
}
coordpdb protein_$i.pdb P$i

segment H$i ...

...

patch ___ P$i H$i (whatever else you may need here)...

etc.
}

On Jun 3, 2008, at 11:47 AM, Katherine Parra wrote:

> Dear VMD community:
> I need to create a PSF file containing several PDB files.
> I used the mergepdbs script published in the scripts library but it
> did not work. The problem is:
> I have 54 pdb files. 18 proteins 18 heme groups and 18 ligands.
> I need 18 segments, each one should contain:1 protein patched to 1
> heme group patched to 1 ligand, in order to have 18 identical
> proteins in the same psf file, keeping the 3 different structures
> bounded by patches.
> Is that possible? What could I do?
>
> Thanks for your attention.
> KP