Subject: CCL:md rookie update

From: "David R. Langley" <[email-masked]>
Date: Thu, 08 Jan 1998 10:30:16 -0500

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:  [email-masked]
phone:  (203) 284-6656 
fax:    (203) 284-7702