VMD-L Mailing List

From: B (m-koshino_at_aist.go.jp)
Date: Wed Nov 11 2020 - 19:40:09 CST

Hello, Raman

As questioned a little bit before, I hope you already solved the problem.
When I encounter the same issue I carefully check my psf and pdb files, with regard to the discrepancy of segname/resid between the two files.
It was also pointed out in the previous ML as attached.

Best regards,

M. Koshino
________________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Sent: Monday, July 9, 2018 23:35
To: vmd-l_at_ks.uiuc.edu; mcg05004_at_byui.edu
Subject: vmd-l: RE: Merge Structures Bug

Repeated segnames or resid/segname combinations. Behind the scenes, merge structures is using psfgen. So if you have repeated segname/resid combinations, only the last one will have coordinates assigned.

-Josh

On 2018-07-06 16:38:31-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

When I try to merge my protein/membrane/ion pdb with my ligand pdb using the merge structures plugin, the merged pdb has the correct coordinates for the ligand, but the coordinates for the protein, membrane, and ions has all zeroes in their columns. I don't get any errors during the merge process, it just seems to erase the coordinates except for the ligand. What might be causing this? Thanks!

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602

________________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Raman Preet Singh <ramanpreetsingh_at_hotmail.com>
Sent: Thursday, August 13, 2020 2:47
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: RE: Merge Structure changes coordinates to 0

Dear All,

I am stuck with the issue listed in the email below. Any directions in resolving the issue will be extremely helpful.

The Multicomponent Assembler in charm-gui.org assembles the protein and graphene or oligosaccharide and graphene correctly but the Merge Structure module in VMD fails.

Regards,
Raman

From: Raman Preet Singh<mailto:ramanpreetsingh_at_hotmail.com>
Sent: 03 August 2020 13:02
To: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Merge Structure changes coordinates to 0

Dear All,

I have generated a graphene model using charmm-gui.org. The graphene structure appears normal when viewed in VMD. However, when I combine graphene with my protein using Merge Structures plugin in VMD, the coordinates of all graphene atoms (carbons and hydrogens) change to 0,0,0 in the x,y,z coordinates. The protein structure appears normal in the combined file and coordinates of protein atoms in the combined pdb are the same as in the initial protein pdb.

An example of how coordinates appear in the initial graphene.pdb and the merged.pdb are below.

Initial coordinates:
ATOM 1 C2 GP0 G 1 -6.167 -5.698 -0.000 1.00 0.00 GP00
ATOM 2 C3 GP0 G 1 -4.934 -6.410 -0.000 1.00 0.00 GP00

Coordinates in the merged file:
ATOM 2872 C2 GP00 1 0.000 0.000 0.000 -1.00 0.00 GP00
ATOM 2873 C3 GP00 1 0.000 0.000 0.000 -1.00 0.00 GP00

I tried this by combining the graphene model with an oligosaccharide and again the graphene coordinates appear zero.

Please help resolve the issue.

Regards,
Raman