VMD-L Mailing List

From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Wed Mar 30 2016 - 23:51:00 CDT

Hi Akshay,
               You could try with "Extensions>modeling>mergestructures".

All the best

On Thu, Mar 31, 2016 at 9:38 AM, Akshay Bhatnagar <
akshaybhatnagar2790_at_gmail.com> wrote:

> Hello everyone
>
> I am creating a tcl script to create psf files for all the pdb file in the
> directory. But when there are more than one chain in the PDB, the program
> is creating psf for only the 'A' chain. To overcome this i used the chain
> id to separate the psf files for each chain of a pdb file. Now, how can i
> concatenate the generated psf.pdb files for two chains of a PDB file.
>
> Also, the second problem i am facing is that chain B is saved with chain
> id 0 identifier , whereas, chain A is saved with chain id 1 identifier, i
> was expecting the reverse. i.e the psf.pdb file with chain A should have a
> lower id in the file name.
>
> The script used is:
>
> package require autopsf
> psfcontext reset
> topology top_all27_prot_lipid.inp
> set filelist [glob *.PDB]
> foreach file $filelist {
> mol new $file
> set name [file rootname $file]
> set selp [atomselect top "not hetero"]
> set chains [lsort -unique [$selp get pfrag]]
> foreach chain $chains {
> set sel [atomselect top "pfrag $chain"]
> $sel writepdb $file-$chain.pdb
> echo "$chain"
> pdbalias residue HIS HSP
> pdbalias atom ILE CD1 CD
> pdbalias atom LYS 1HZ HZ1
> pdbalias atom LYS 2HZ HZ2
> pdbalias atom LYS 3HZ HZ3
> pdbalias atom ARG 1HH1 HH11
> pdbalias atom ARG 2HH1 HH12
> pdbalias atom ARG 1HH2 HH21
> pdbalias atom ARG 2HH2 HH22
> pdbalias atom ASN 1HD2 HD21
> pdbalias atom ASN 2HD2 HD22
> pdbalias atom SER HG HG1
> segment U {pdb $file-$chain.pdb}
> coordpdb $file-$chain.pdb U
> guesscoord
> writepdb $file-$chain-psf.pdb
> resetpsf
> }
> }
>
>
>
> With Regards
> Akshay Bhatnagar
> PhD Student
> BITS Pilani Hyderabad Campus
>
>