PDB format questions(in OpenMM Zephyr)

OpenMM Zephyr provides a visual application for running GPU-accelerated molecular simulations.
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Cho yunsung
Posts: 8
Joined: Sun Jul 26, 2009 4:20 pm

PDB format questions(in OpenMM Zephyr)

Post by Cho yunsung » Sun Aug 23, 2009 11:17 pm

Hi.

I installed OpenMM Zephyr and have tested sample pdb file.

But, when I tried to test my PDB file this program didn't work(Error while converting PDB file)
I tried to change like OpenMM Zephyr manual
(CYS->CYN
HIS->HID
LYS->LYP
and N-ter, C-ter.)
But also, it didn't work.
Please, help me!
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Christopher Bruns
Posts: 32
Joined: Thu Apr 07, 2005 1:10 pm

RE: PDB format questions(in OpenMM Zephyr)

Post by Christopher Bruns » Tue Sep 15, 2009 8:41 am

The next version of Zephyr will help by automatically renaming the residues and atoms.

Are there any error messages from the pdb2gmx step in the log window of the status tab of Zephyr? (Or equivalently in the zephyr.log file?)
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