AMBER Archive (2005)

Subject: Re: AMBER: tleap load pdb file

From: David A. Case (case_at_scripps.edu)
Date: Fri Feb 04 2005 - 16:45:50 CST

On Fri, Feb 04, 2005, xiaowen wrote:

> I modify nuc.in to:
> ******************************************
> NUC 1
> D
> A5 A A A A3
> NUC 2
> T5 T T T T3
> END
> $ABDNA
> *******************************************
> $AMBERHOME/exe> nucgen -O -i nuc2.in -o nuc2.out -d
> $AMBERHOME/dat/leap/parm/nucgen.dat -p nuc2.pdb
>
> so far is fine, the nuc2.pdb can be open by internet Explorer.

The question is really, what is in this pdb file? Can you post it? 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.

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

...dac

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