Re: Issue Combining PSF and PDB Files

From: Daipayan Sarkar (
Date: Sun Nov 13 2022 - 21:11:06 CST

Hi Collin,
If you split the structure such that four chains have different psf and
pdb, then you can use topotools to merge them. You should do this before
solvating and adding counter ions. You can read more about how to merge
molecules using topotools here

Based on the example provided in the link I shared above, if you have four
chains (part1-4), you could try the following. Here, part1-4.psf and
corresponding pdb's are only for the individual chains.
package require topotools
# load to be merged molecules into VMD
set midlist {}
set mol [mol new part1.psf waitfor all]
mol addfile part1.pdb
lappend midlist $mol
set mol [mol new part2.psf waitfor all]
mol addfile part2.pdb $mol
lappend midlist $mol
set mol [mol new part3.psf waitfor all]
mol addfile part3.pdb $mol
lappend midlist $mol
set mol [mol new part4.psf waitfor all]
mol addfile part4.pdb $mol
lappend midlist $mol
# do the magic
set mol [::TopoTools::mergemols $midlist]
animate write psf merged.psf $mol
animate write pdb merged.pdb $mol

Once you have merge.psf and merge.pdb, you can now solvate and ionize as
you were doing earlier.


On Sun, Nov 13, 2022 at 8:38 PM Collin Nisler <> wrote:

> Hello, I am encountering a strange issue when I try to combine multiple
> psf an pdb files. I have four chains, each saved as separate psf and pdb
> files. I have solvated and ionized each chain separately, as a test, and I
> am able to simulate each separately perfectly fine without issue. When I
> try combining all into one psf and pdb, either by using the "readpsf" and
> "coordpdb" command in the tkconsole, the MergeStructs plugin, or by using a
> psfgen script on just the pdb files, I encounter the "bad global angle" and
> "bad global dihedral count" errors when I try simulating the complete
> system. I checked the psf files, and the correct number of angles and
> dihedrals are present in each case, and there are no obvious issues when I
> visually inspect the structure. Based on the fact that each runs fine
> alone, I have to conclude that it is the process of combining all that
> results in the error, but I am at a complete loss for where the error comes
> from or even what the source of the error is. Any insight into this issue
> would be greatly appreciated. Thanks.
> Collin

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