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solvating protein in a water box
#19256 11/06/08 07:42 AM
Joined: Feb 2008
Posts: 62
Ramya Offline OP
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Joined: Feb 2008
Posts: 62
Hi all,
I am using Charmm version 33b2. I solvated the protein crambin using the script solvent-box.str. But the protein is going out the box. I have enclosed the input script here. Please point out the error in it.
!level of tolerance
bomlev -1

!get the topology file
open read unit 1 name top_all22_prot.inp card
read rtf card unit 1
close unit 1

!get the parameter file
open read unit 2 name par_all22_prot.inp card
read para card unit 2
close unit 2

!read the peptide pdb file
open read unit 3 name crambin.pdb card
read sequence pdb unit 3
generate prot setup
patch glup prot 23
patch aspp prot 43
patch disu prot 3 prot 40 setu sort warn
patch disu prot 4 prot 32 setu sort warn
patch disu prot 16 prot 26 setu sort warn
rewind unit 3
read coord pdb unit 3
close unit 3

ic fill preserve
ic parameter
ic build

!write outputs
write coor card name "cram.crd"
write coor pdb name "cram.pdb"
write psf card name "cram.psf"

!compute intramolecular energy of peptide
set te ?ener

!To solvate the peptide
set XSIZ 27.0set YSIZ 30.0
set ZSIZ 35.0

!define SOLUTE sele segid prot end
stream solvent-box.str
cons harm force 50.0 sele SOLUTE end
mini sd nstep 50

!write the output files with water
write coor pdb name cramsol.pdb
write psf card name cramsol.psf
write coor card name cramsol.crd


I tried it by even changing the xyz sizes, but I am getting segmentation fault.

Re: solvating protein in a water box
Ramya #19257 11/06/08 08:09 AM
Joined: Sep 2003
Posts: 4,794
Likes: 2
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Joined: Sep 2003
Posts: 4,794
Likes: 2
I am not quite sure what your problem is, but it seems that you find that the protein is not completely within the box. You have decided to use the box dimensions given in the usage example in solvent-box.str, and this may not be appropriate for crambin. You have to change the dimensions to suite your problem. Note that a rhombic dodecahdron (RHDO), which is symmetric, may be a better shape than a cube or a prism since its volume is smaller for a given distance between the primary solute and its images. There are examples of how to setup the RHDO in the Script Archive.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  lennart, rmv 

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