Systems with multiple segments in CHARMM.

If you read through my blog, you will see I did post one blog about setting up PEG in a TIP3P water box with CHARMM ether force field.

 

I got new tasks from my dear advisor. Two PEGs in one TIP3P water box. In AMBER, this is pretty simple, I just need to prepare a PDB files contains two PEG and add TER between the two molecules. Never mind, my story in this blog is using CHARMM ether force field for PEG. By the way, PEG with GAFF seemed not that rational compared with that using CHARMM ether force field.

 

As a beginner of CHARMM, the learning process is really painful. I got help from CHARMMing.org. I used a multiple chains protein in PDB as input files, and look into the input scripts. I find the clue that CHARMM will generate multiple PSF files for each segments at the beginning, and then attached all PSF files together as a whole.

 

Based on the script from the website, I tried several times and got the answer. The following procedure is what I used for the system.

  1. I got the PDB files of one PEG from my previous simulation.
  2. Use VMD to prepare two PEG PDB files with proper coordinates.
  3. Save the two PEG PDB files separately as 1.pdb and 2.pdb.
  4. Use the following 1.inp to generate 1.psf, and change 1 to 2 and generate 2.psf.
  5. Use combine.inp to generate two PEG vacuum PSF file.
  6. Use VMD to generate PSF and PDB of the water box.

 

1.inp

* Run Segment Through CHARMM
*

dimension chsize 1500000

prnlev 5
wrnlev 5
bomlev -1

! read topology and parameter files

wrnlev 1
wrnlev 5

read rtf card name ../top_all35_ethers-oh.rtf
read param card name ../par_all35_ethers-oh.prm





read sequence pdb name 1.pdb
generate a-good setu first GCL0 last GCL3 noangle nodihedral

read coor pdb name 1.pdb

hbuild

! write out the protein structure file (psf) and
! the coordinate file in pdb and crd format.

write psf card name 1.psf
* PSF
*

write coor card name 1.crd
* Coords
*

write coor pdb name 1_charmm.pdb
* PDB for JSmol visualization
*


stop

 

 

combine.inp

* Append multiple segments into a final structure
*

dimension chsize 1500000

prnlev 5
wrnlev 5
bomlev -1

! read topology and parameter files
read rtf card name ../top_all35_ethers-oh.rtf

wrnlev 1
read param card name ../par_all35_ethers-oh.prm
wrnlev 5





! Read PSF from file
read psf card name 1.psf
read psf card append name 2.psf

autogenerate angles dihedrals

! read coordinates
read coor card name 1.crd
read coor card append name 2.crd




! orient structure
!! BTM, don't do this, it might muck with re-assembling the
!! structure for redox calculations
!coor orient

! calculate energy
energy

ioform extended

write psf card name twoPEGvac.psf
* twoPEGvac.psf
*

write coor card name twoPEGvac.crd
* twoPEGvac.crd
*

write coor pdb name twoPEGvac.pdb
* twoPEGvac.pdb
*


stop

 

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