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
COOR STATISTICS SELE ( SEGID bulk ) END
! write out the psf and the coordinates
open unit 1 write formatted name firstname.lastname@example.org
write psf card unit 1
open unit 1 write formatted name email@example.com
write coordinate pdb unit 1
Can anyone explain me what is wrong? Thanks for your help.