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.

Sonal Gahlawat
Ph.D. Student
Department of Biomedical Engineering, Rutgers University
599 Taylor Rd, Piscataway, NJ 08854