Subject: more summary about adding hydrogen

From: Mao Xiang <[email-masked]>
Date: Wed, 22 Nov 2000 08:45:12 +0800

Hi:

   Here is another two email replying my questoin that I forgot to put
them in my last eamil. Thanks.

----------------
From: Deepak Singh <[email-masked]>

Hi

YOu should theoretically not need to use HBUILD.

Just use

IC PARAM
IC BUILD

where you used HBUILD.

From: [email-masked]>

I am not an expert, either. However, I could solve this problem by
addition of the sgment name to the lines of coordinate. For example you
are generating "PROT" segment. In this case, I think CHARMM tries to
find
the corresponding coordinate for the atom, the residue, and the segment
as
specified in psf file. If you look at the first error, there is nothing
for segname:

 ** WARNING ** For atom in coordinate file, could not find residue in
PSF, and is thus ignored:

  SEGID=     RESID=1    RESNAME= GLU  TYPE= N   
 *** LEVEL  1 WARNING *** BOMLEV IS    0

I edited the pdb file and added the segname at the end of the coordinate
lines. Then it worked. The format is fixed. Use the following line as an
example (If the line is broken to two line, it is because of my editor, 
join them first):

ATOM      1  N   ALA A  19     158.405  67.834  38.687  1.00101.61
PROT

  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|  Xiang Mao                                                     |
|  Lab of Molecular Regulation for Microbial Secondary Metabolism |
|  Shanghai institute of Plant Physiology, Academia Sinica        |
|  300 Fenglin Road, Shanghai, China, 200032                      |
|  Tel: +86-21-64042090-4791                                      |
|  Fax: +86-21-64042385                                           |
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~