Re: AMBER: tleap load pdb file

From: xiaowen <xwfang.iastate.edu>
Date: Sat, 5 Feb 2005 11:20:12 -0600 (CST)

Thanks David,

> The question is really, what is in this pdb file? Can you post it?
I attached the amberusing.rar to this email. It includes config.h, nuc.pdb
(which is an original pdb file generated by the nuc.in), nuc2.pdb (which is
the smaller DNA pdb file), make serial.log (which is the .log file for
compiling amber8), test tleap.log (which is the test leap .log file)


>Have you compared it to a DNA pdb file from the PDB itself? The fact that
LEaP thinks
> you have a chainid (not a residue name) of "T" suggests that some items might
> not be in the right column.

I have compared nuc.pdb with the one on tutorial website. they are same.

> Also, please provide more information about your OS and machine. What
options did you give to the configure script?

$AMBERHOME/src> ./configure xlf90_aix

so generate config.h file

system.info includes the system information, I put it also in the attachment.

Thanks and have a good weekend!
Xiaowen






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Received on Sat Feb 05 2005 - 17:53:01 PST
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