Subject: About Charmm Minimization

From: Liu Zhijie <[email-masked]>
Date: Fri, 28 May 1999 20:47:31 -0700 (PDT)

Dear all,

   When I use CHARMM97 to minimize the protein structures, coordinates 
of the water molecules (include associated water and solvent water ) and 
the metal ions can not be setup and read in. 
Since the topology files AMINO.BIN and IONS.RTF include these 
segments , there may are some problems in my input file. Please examine 
the head of my input file and give your oppinions,  any help will be 
appreciate.

-------------------------------------------------------
BOML -1                                               |
                                                      |
OPEN READ UNIT 11 FILE NAME "$CHM_DATA/AMINO.BIN"     |
READ RTF UNIT 11 FILE                                 |
CLOSE UNIT 11                                         |
                                                      |
OPEN READ UNIT 12 FILE NAME "$CHM_DATA/PARM.BIN"      |
READ PARAMETERS UNIT 12 FILE                          |
CLOSE UNIT 12                                         | 
                                                      |
OPEN READ UNIT 13 CARD NAME "$CHM_DATA/IONS.RTF"      |
READ PARAMETERS UNIT 13 CARD                          |
CLOSE UNIT 13                                         | 
                                                      |
OPEN READ UNIT 14 CARD NAME x.pdb                     |
READ SEQUENCE PDB UNIT 14                             |
                                                      |
GENERATE XXXX SETUP                                   |
                                                      |
REWIND UNIT 14                                        |
                                                      |
READ COORDINATES PDB UNIT 14                          |
CLOSE UNIT 14                                         |
-------------------------------------------------------
   Sincerely yours

   Liu Zhijie

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---

From: Deepak Singh <[email-masked]>
Date: Fri, 28 May 1999 10:54:49 -0400

Dear LIu,

You should read in the second RTF before reading in the parameters.  Also the read
command for ions.rtf should be read rtf and NOT read para.  It should be

READ RTF UNIT 13 CARD APPEND\

Regards

Deepak.

Liu Zhijie wrote:

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--
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---

From: Deepak Singh <[email-masked]>
Date: Fri, 28 May 1999 11:51:21 -0400

There is a slight ypo in my message ... Ignore the \ after  "APPEND"

Deepak.