AMBER Archive (2002)

Subject: Re: crdgrow

From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Tue Oct 08 2002 - 12:24:09 CDT

I am sorry if I am of no help, for I can make only suggestions.

1. what is the correct format of a prepin file name to use with crdgrow
(I've tried the one on page 74 and I got a core dumped error message). I
would appreciate if someone could send me the prepin file for an
aminoacid.
+++ Core dumping is a problem tracking which is never easy except for
those who wrote the code. May be you can try on some other operating
system for a change, to see if it is not more robust compiler to look over
certain 'standard' mistakes. It 'might' help.

2. when I load a pdb structure in LEaP it will automatically add missing
atoms and hydrogens. Is there a feature to use to tell LEaP not to add the
hydrogens (I mean I can always write out the pdb file, edit the text file
and remove the hydrogens myself but it would be easier if I could tell
LEaP just not to do this)?
+++ You can make the first PDB using leap, and then edit that output.
Since these atoms won't be 'missing atoms' when you feed it again to leap,
it might accept the coordinates.

With best wishes,
-Sanjeev