VMD-L Mailing List

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Wed Aug 12 2020 - 12:47:51 CDT

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