From: SEKIJIMA Masakazu <m.sekijima_at_aist.go.jp>
Date: Thu 30 May 2002 17:43:14 +0900

Dear Amber Users:

I would like to use TIP4P model insted of TIP3P.

So Amber7 User's manual says that
1st step) solvate the system, using the default TIP3 model
2nd step) use ambpdbto convert your prmtop file to Brookhaven format
3rd step) restart LEaP, choose the TIP4P water model, then use
loadPdb to bring back om the system you have created.

Then I made test peptide like below (First Step).
> pep = sequence {ALA ALA ALA}
> SolvateBOX pep WATBOX216 1
  Solute vdw bounding box: 12.851 10.225 7.236
  Total bounding box for atom centers: 14.851 12.225 9.236
  Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 1 y= 1 z= 1
Adding box at: x=0 y=0 z=0
Center of solvent box is: 0.000000, 0.000000, 0.000000
  Total vdw box size: 16.103 14.768 12.128 angstroms.
  Volume: 2883.995 A^3
  Total mass 537.528 amu, Density 0.310 g/cc
  Added 18 residues.
> saveAmberParm pep pep.top pep.crd


After I made amber parmfiles, I tryed to convert prm format to PDB
format (2nd Step).
% ambpdb -p pep.top -aatm
| New format PARM file being parsed.
| Version = 1.000 Date = 05/30/02 Time = 16:14:49

But I could not complete this step, because I did not finish
this calculation in 2 hours. I think this target peptide is
small. If someone know the reason, please teach me.

And... If I can make PDB format file (pep.pdb),
I think 3rd step will be like below. Is that right?

>WAT = TP4
>loadAmberParams frcmod.tip4p
>set WAT.1 name "TP4"
>pep = LoadPdb pep.pdb
>saveAmberParms pep pep.top pep.crd

Best Regards!

Masakazu SEKIJIMA, Ph.D.
Computational Biology Research Center (CBRC)
National Institute of Advanced Industrial Science and Technology (AIST)
Received on Thu May 30 2002 - 01:43:14 PDT
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