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From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Mon Aug 03 2020 - 01:58:25 CDT

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