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#820 01/09/04 07:44 AM
Joined: Dec 2003
Posts: 80
L
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L
Joined: Dec 2003
Posts: 80
Hi, all
I builded th dsDNA structure"CATG-CATG-CATG" . And I creat a water box (30* 18 *18 A).But it's still error.Could someone tell me how to fix my error ?
thank you
yeng-tseng


script
***************************************************************
* Solvate the protein Echistatin by a water sphere
* EMBNet Course on Molecular Dynamics Simulation
* by R. Stote, A. Dejaegere, L. Falquet, D. Kuznetsov
*

! Read in Topology and Parameter files

open unit 1 card read name top_all27_na.rtf
read RTF card unit 1
close unit 1

open unit 1 card read name par_all27_na.prm
read PARA card unit 1
close unit 1

! Read PSF file
open unit 1 card read name cagt.psf
read psf card unit 1

! Read in energy minimzed coordinates
open unit 1 read formatted name cagt.pdb
read coor pdb unit 1
close unit 1

! To Begin, translate the system to insure it is at the origin }
define origin select all end

! { find the centre of the reaction region }
coordinate statistics select ( origin ) end

! { make this point the origin }
coordinate translate xdirection -?XAVE ydirection -?YAVE zdirection -
?ZAVE

! { verify }
coordinate statistics select ( origin ) end

! Read in water sphere sequence
open unit 1 read formatted name solvenbox70.crd
read sequence coor unit 1
rewind unit 1

! Generate new segment for the water sphere
generate bulk noangle nodihedral

! Read water sphere coordinates
read coor card unit 1 append
close unit 1


! center the water sphere
coordinate orient noro select segid bulk end

! Delete waters which overlap with protein }
delete atom sort -
select .byres. (segid bulk .AND. type oh2 .and. -
((.not. (segid A:B .OR. hydrogen)) .around. 2.8)) end

! Delete all water beyond the outer cutoff
delete atom sort -
select .byres. ( .not. ( point 0. 0. 0. cut 30.0) -
.and. ( segid bulk .AND. type oh2 ) ) end

! End of solvation of system



open unit 1 card write name catg-water.psf
write psf card unit 1
* solvated echestatin
*
close unit 1

open unit 1 card write name catg-water.pdb
write coor pdb unit 1
* echestatin Structure with hydrogens
*
close unit 1

stop

*******************************************************************
error message


CHARMM> ! Delete waters which overlap with protein }
CHARMM> delete atom sele .byres. (segid wat .and. (.not. hydrogen) .and. -
CHARMM> (((segid A:B) .and. .not. hydr) .around. 1.6)) end
SELRPN> 0 atoms have been selected out of 8527

label #821 01/09/04 08:46 AM
Joined: Sep 2003
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Is the segid of your waters WAT (as in the output you show) or BULK (as in the input file)? Are the water molecules and the DNA overlapping (coor stat ..., or visual inspection)? General tip in debugging selections is to reduce the complexity of the selection, and then add things one at a time:

define junk sele segid wat end
define junk sele .not. segid wat .around 1.6 end
define junk sele segid wat .and (.not. segid wat .around 1.6 ) end
...


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  BRBrooks, lennart, rmv 

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