VMD-L Mailing List

From: SONAL GAHLAWAT (sg1389_at_scarletmail.rutgers.edu)
Date: Mon Apr 17 2023 - 11:42:20 CDT

Hello VMD Users,

I am working on doing steered MD on collagen-like peptides. After reviewing
the psgfen tutorial, I created three different pairs of psf and pdb files
for each chain of the molecule (Chain A, B, and C) using the same topology
file (top_all36_prot.rtf). In the next step, I want to combine the three
pairs of psf and pdb files to solvate the protein for minimization and
steered MD. However, I am getting errors in combining the psf files.

My basic script is:

package require psfgen
readpsf 1k6f_A.psf pdb 1k6f_A.pdb
readpsf 1k6f_B.psf pdb 1k6f_B.pdb
readpsf 1k6f_C.psf pdb 1k6f_C.pdb

After entering the second line, I get the following error.

psfgen) reading structure from psf file 1k6f_A.psf
psfgen) reading coordinates, insertion codes, and element symbols from pdb
file 1k6f_B.pdb
psfgen) duplicate topology file D:/SMD/1K6F/top_all36_prot.rtf
psfgen) Unable to add (duplicate?) residue CHA:1

I would really appreciate it if someone can help me troubleshoot this.
Thank you.

Regards,
Sonal Gahlawat
Ph.D. Student
Department of Biomedical Engineering, Rutgers University
599 Taylor Rd, Piscataway, NJ 08854
Email: sg1389_at_scarletmail.rutgers.edu