AMBER Archive (2002)

Subject: Re: TIP4P

From: SEKIJIMA Masakazu (m.sekijima_at_aist.go.jp)
Date: Fri May 31 2002 - 02:32:08 CDT

Dear Amber Users:

Yesterday's my question's goal was:

> I would like to use TIP4P model insted of TIP3P.

And... Because of kindly help, I passed below's
1st and 2nd steps.

> 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.

In my test, I made tripeptide {ALA ALA ALA} surrounded
by TIP3P water by LEaP. Then I made Pdb-file by below
command and options.

% ambpdb -pqr -p pep.top < pep.crd > pep.pdb

I have not used TIP4P model yet, because I could not pass 3rd step.
What should I do to overcome below warning message and
to use TIP4P model? Should I need to relax TIP3P model
water before restart LEaP?

Thanks.
---------------------------------------------------------------
% tleap
-I: Adding /usr/local/amber7/dat/leap/prep to search path.
-I: Adding /usr/local/amber7/dat/leap/lib to search path.
-I: Adding /usr/local/amber7/dat/leap/parm to search path.
-I: Adding /usr/local/amber7/dat/leap/cmd to search path.

Welcome to LEaP!
Sourcing leaprc: /usr/local/amber7/dat/leap/cmd/leaprc
Log file: ./leap.log
Loading parameters: /usr/local/amber7/dat/leap/parm/parm96.dat
Loading library: /usr/local/amber7/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber7/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber7/dat/leap/lib/solvents.lib
> WAT = TP4
> LoadAmberParams frcmod.tip4p
Loading parameters: /usr/local/amber7/dat/leap/parm/frcmod.tip4p
Reading force field mod type file (frcmod)
> set WAT.1 name "TP4"
> pep = Loadpdb pep.pdb
Loading PDB file: ./pep.pdb
Created a new atom named: H within residue: .R<NALA 1>
  Added missing heavy atom: .R<CALA 3>.A<OXT 11>
  total atoms in file: 84
  Leap added 22 missing atoms according to residue templates:
       1 Heavy
       21 H / lone pairs
  The file contained 1 atoms not in residue templates
> check pep
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 4>.A<O 3> and .R<TP4 4>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 5>.A<O 3> and .R<TP4 5>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 6>.A<O 3> and .R<TP4 6>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 7>.A<O 3> and .R<TP4 7>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 8>.A<O 3> and .R<TP4 8>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 9>.A<O 3> and .R<TP4 9>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 10>.A<O 3> and .R<TP4 10>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 11>.A<O 3> and .R<TP4 11>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 12>.A<O 3> and .R<TP4 12>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 13>.A<O 3> and .R<TP4 13>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 14>.A<O 3> and .R<TP4 14>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 15>.A<O 3> and .R<TP4 15>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 16>.A<O 3> and .R<TP4 16>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 17>.A<O 3> and .R<TP4 17>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 18>.A<O 3> and .R<TP4 18>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 19>.A<O 3> and .R<TP4 19>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 20>.A<O 3> and .R<TP4 20>.A<EPW 4>
WARNING: There is a bond of 0.150000 angstroms between:
------- .R<TP4 21>.A<O 3> and .R<TP4 21>.A<EPW 4>
FATAL: Atom .R<NALA 1>.A<H 13> does not have a type.
Warning: Close contact of 0.032424 angstroms between .R<NALA 1>.A<H1 2> and .R<NALA 1>.A<H 13>
Warning: Close contact of 1.018865 angstroms between .R<NALA 1>.A<N 1> and .R<NALA 1>.A<H 13>
Warning: Close contact of 0.761895 angstroms between .R<TP4 4>.A<EPW 4> and .R<TP4 4>.A<H2 2>
Warning: Close contact of 0.763649 angstroms between .R<TP4 4>.A<EPW 4> and .R<TP4 4>.A<H1 1>
Warning: Close contact of 0.763558 angstroms between .R<TP4 5>.A<EPW 4> and .R<TP4 5>.A<H2 2>
Warning: Close contact of 0.762869 angstroms between .R<TP4 5>.A<EPW 4> and .R<TP4 5>.A<H1 1>
Warning: Close contact of 0.763052 angstroms between .R<TP4 6>.A<EPW 4> and .R<TP4 6>.A<H2 2>
Warning: Close contact of 0.762496 angstroms between .R<TP4 6>.A<EPW 4> and .R<TP4 6>.A<H1 1>
Warning: Close contact of 0.762778 angstroms between .R<TP4 7>.A<EPW 4> and .R<TP4 7>.A<H2 2>
Warning: Close contact of 0.762147 angstroms between .R<TP4 7>.A<EPW 4> and .R<TP4 7>.A<H1 1>
Warning: Close contact of 0.762518 angstroms between .R<TP4 8>.A<EPW 4> and .R<TP4 8>.A<H2 2>
Warning: Close contact of 0.763914 angstroms between .R<TP4 8>.A<EPW 4> and .R<TP4 8>.A<H1 1>
Warning: Close contact of 0.763557 angstroms between .R<TP4 9>.A<EPW 4> and .R<TP4 9>.A<H2 2>
Warning: Close contact of 0.762080 angstroms between .R<TP4 9>.A<EPW 4> and .R<TP4 9>.A<H1 1>
Warning: Close contact of 0.763752 angstroms between .R<TP4 10>.A<EPW 4> and .R<TP4 10>.A<H2 2>
Warning: Close contact of 0.763651 angstroms between .R<TP4 10>.A<EPW 4> and .R<TP4 10>.A<H1 1>
Warning: Close contact of 0.763051 angstroms between .R<TP4 11>.A<EPW 4> and .R<TP4 11>.A<H2 2>
Warning: Close contact of 0.762658 angstroms between .R<TP4 11>.A<EPW 4> and .R<TP4 11>.A<H1 1>
Warning: Close contact of 0.763183 angstroms between .R<TP4 12>.A<EPW 4> and .R<TP4 12>.A<H2 2>
Warning: Close contact of 0.762617 angstroms between .R<TP4 12>.A<EPW 4> and .R<TP4 12>.A<H1 1>
Warning: Close contact of 0.762930 angstroms between .R<TP4 13>.A<EPW 4> and .R<TP4 13>.A<H2 2>
Warning: Close contact of 0.764977 angstroms between .R<TP4 13>.A<EPW 4> and .R<TP4 13>.A<H1 1>
Warning: Close contact of 0.763764 angstroms between .R<TP4 14>.A<EPW 4> and .R<TP4 14>.A<H2 2>
Warning: Close contact of 0.762805 angstroms between .R<TP4 14>.A<EPW 4> and .R<TP4 14>.A<H1 1>
Warning: Close contact of 0.763238 angstroms between .R<TP4 15>.A<EPW 4> and .R<TP4 15>.A<H2 2>
Warning: Close contact of 0.763063 angstroms between .R<TP4 15>.A<EPW 4> and .R<TP4 15>.A<H1 1>
Warning: Close contact of 0.762990 angstroms between .R<TP4 16>.A<EPW 4> and .R<TP4 16>.A<H2 2>
Warning: Close contact of 0.763570 angstroms between .R<TP4 16>.A<EPW 4> and .R<TP4 16>.A<H1 1>
Warning: Close contact of 0.762375 angstroms between .R<TP4 17>.A<EPW 4> and .R<TP4 17>.A<H2 2>
Warning: Close contact of 0.763931 angstroms between .R<TP4 17>.A<EPW 4> and .R<TP4 17>.A<H1 1>
Warning: Close contact of 0.762552 angstroms between .R<TP4 18>.A<EPW 4> and .R<TP4 18>.A<H2 2>
Warning: Close contact of 0.762719 angstroms between .R<TP4 18>.A<EPW 4> and .R<TP4 18>.A<H1 1>
Warning: Close contact of 0.762380 angstroms between .R<TP4 19>.A<EPW 4> and .R<TP4 19>.A<H2 2>
Warning: Close contact of 0.763703 angstroms between .R<TP4 19>.A<EPW 4> and .R<TP4 19>.A<H1 1>
Warning: Close contact of 0.764570 angstroms between .R<TP4 20>.A<EPW 4> and .R<TP4 20>.A<H2 2>
Warning: Close contact of 0.762856 angstroms between .R<TP4 20>.A<EPW 4> and .R<TP4 20>.A<H1 1>
Warning: Close contact of 0.762629 angstroms between .R<TP4 21>.A<EPW 4> and .R<TP4 21>.A<H2 2>
Warning: Close contact of 0.762890 angstroms between .R<TP4 21>.A<EPW 4> and .R<TP4 21>.A<H1 1>
Checking parameters for unit 'pep'.
Checking for bond parameters.
Checking for angle parameters.
check: Errors: 1 Warnings: 56

_________
Masakazu SEKIJIMA, Ph.D.
m.sekijima_at_aist.go.jp
Computational Biology Research Center (CBRC)
National Institute of Advanced Industrial Science and Technology (AIST)