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#1139 - 03/26/04 01:46 PM Wrong output PDB and PSF files
DamienBB Offline
Forum Member

Registered: 03/25/04
Posts: 7
Loc: Detroit, MI, USA
I am not very familiar with CHARMM yet. I would like to create a cubic box filled with Methyl Methacrylate (MMA). I found the PDB file for one molecule, created another PDB file for 512 moledules and then converted this file into a CRD. Now I would like to heat my system and/or minimize the energy.
I found a tutorial explaining how to create a water box. I followed the instruction, renamed the files appropriately and as a result I get water molecules instead of MMA!
Here is the code I am using to create the box...

* Generate PSF for MMA

! read the topology and parameter file
open read formatted unit 12 name top_all22_prot.inp
read rtf card unit 12
open read formatted unit 12 name par_all22_prot.inp
read para card unit 12

! Generate MMA psf and coordinates
set 4 bulk ! MMA identified

open unit 1 read formatted name tip3p.crd
! read box of MMA
read sequence unit 1 coor
rewind unit 1
! generate new segment id and psf
generate bulk noangle nodihedral
! read MMA box coordinates
read coor card unit 1
close unit 1

! verify location of MMA box

! write out the psf and the coordinates
open unit 1 write formatted name scr/@4.psf
write psf card unit 1

open unit 1 write formatted name scr/@4.pdb
write coordinate pdb unit 1
* COORdinates

Can anyone explain me what is wrong? Thanks for your help.
Damien A. Bernard-Brunel Graduate student Dept. of Chemical Engineering Wayne State University Detroit, MI

#1140 - 03/31/04 10:40 PM Re: Wrong output PDB and PSF files [Re: DamienBB]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8419
Loc: 39 03 48 N, 77 06 54 W
Did you create your own MMA residue and add it to the file top_all22_prot.inp? I don't believe that molecule is available in any of the standard CHARMM topology files. You may still have some work to do-- namely create and test a new residue for the molecule you wish to study.
Rick Venable
computational chemist


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