VMD-L Mailing List

From: root (root_at_liposome.genebee.msu.su)
Date: Thu Jan 08 1998 - 12:42:37 CST

---------- Forwarded message ----------
Date: Thu, 08 Jan 1998 10:30:16 -0500
From: "David R. Langley" <david_at_viper.wf.bms.com>
To: root_at_liposome.genebee.msu.su
Cc: chemistry_at_infomeister.osc.edu
Subject: CCL:md rookie update

Hi,

The best wat to go from a charmm DCD formate (machine-dependent) to a
machine-independent formate and then back to the DCD formate is to use
charmm. The following is a charmm input file for such conversions.

* d(ccaacgttgg)2 + 18 NA + 1335 waters. D.R. Langley 2-12-97
*
! Startup script for CHARMm
!
UPPER ! case for files to write
!open write card unit 7 name DNA.LOG
!outu 7
banner
bomblevel -2
wrnlev 5
prnlev 5
open read card unit 21 name "DNAPRM/BMS.RTF"
read rtf card unit 21
close unit 21
open read card unit 22 name "DNAPRM/BMS.prm"
read param card unit 22
close unit 22

DELE ATOM SELECT ALL END
read sequ card
* d(ccaacgttgg) strand A
*
   10
C C A A C G T T G G
generate A setup FIRS 5TER LAST 3TER

read sequ card
* d(ccaacgttgg) strand B
*
   10
C C A A C G T T G G
generate B setup FIRS 5TER LAST 3TER

read sequ NA 18
generate C setup noang nodihe

open read unit 21 card name DNA_2.CRD !canonical B-DNA
read coor unit 21 card
close unit 21

!To convert charmm DCD files to a machine-independent formate use next 3 lines.

OPEN READ UNIT 99 FILE NAME DNANA.DCD
OPEN WRITE UNIT 98 CARD NAME DNANA.DHX
DYNA FORM FIRST 99 NUNIT 1 BEGIN 250 SKIP 250 OUTPUT 98

!To convert charmm DHX files back into DCD formate use next 3 lines.

OPEN READ UNIT 99 CARD NAME DNANA.DHX
OPEN WRITE UNIT 98 FILE NAME DNANA.DCD
DYNA UNFORM INPUT 99 OUTPUT 98

STOP 

-- 
David R. Langley, Ph.D.
Bristol Myers Squibb Pharma. Res. Inst. 
Department of Macromolecular Structure  
P.O. Box 5100    Room 458B             
Wallingford, CT  06492
email:  david_at_viper.wf.bms.com
phone:  (203) 284-6656 
fax:    (203) 284-7702