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normal VMD visualization with cg_bonds

  • scott
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8 years 1 week ago #5487 by scott
VMD visualization with cg_bonds was created by scott
I am visualized a CG model with VMD, which contains peptides , lipids, water and Cl- ions. after applying cg_bonds with command
cg_bonds -top x.top -topoltype "elastic"

it shows errors as:

ERROR
invalid atom id
invalid atom id

My .top file and .gro have been running well in gromacs, which shall not have "invalid atom id" in my understanding.
Anybody can help to point out what is going wrong?

Thanks in advance!
DL

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7 years 10 months ago #5682 by jonasori
Replied by jonasori on topic VMD visualization with cg_bonds
Did the cg_bonds command work? It seems like that might be your problem - that command could be wrong. I've also never seen an option put in quotes (like in -topoltype "elastic"); could it be that the program is looking to get -topoltype elastic instead of -topoltype "elastic"?

I'm very new to this, so my suggestions may be pretty far off, but who knows.

Best of luck,

Jonas

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7 years 9 months ago #5706 by peterkroon
Replied by peterkroon on topic VMD visualization with cg_bonds
You can try loading the bonded information from the tpr file rather than from the top file.

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