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PDB format questions(in OpenMM Zephyr)

Posted: Sun Aug 23, 2009 11:17 pm

by jopd83

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!

RE: PDB format questions(in OpenMM Zephyr)

Posted: Tue Sep 15, 2009 8:41 am

by cmbruns

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?)