Re:AMBER: MD simulation on a protein solvated by a combination of some water mod

From: 荒牧 武志 <>
Date: Thu, 14 Jul 2005 09:56:39 +0000

Thank you for your answer

  I tried to create a pdb file as you said. But I couldn't make a pdb
file. I performed leaps command as following.


Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff99
----- Source: /home/aramaki/amber8/dat/leap/cmd/leaprc.ff99
----- Source of /home/aramaki/amber8/dat/leap/cmd/leaprc.ff99 done
Log file: ./leap.log
Loading parameters: /home/aramaki/amber8/dat/leap/parm/parm99.dat
Loading library: /home/aramaki/amber8/dat/leap/lib/all_nucleic94.lib
Loading library: /home/aramaki/amber8/dat/leap/lib/all_amino94.lib
Loading library: /home/aramaki/amber8/dat/leap/lib/all_aminoct94.lib
Loading library: /home/aramaki/amber8/dat/leap/lib/all_aminont94.lib
Loading library: /home/aramaki/amber8/dat/leap/lib/ions94.lib
Loading library: /home/aramaki/amber8/dat/leap/lib/solvents.lib
> mol = loadPdb water_only_tip5p.pdb
Loading PDB file: ./water_only_tip5p.pdb
  total atoms in file: 3
  Leap added 2 missing atoms according to residue templates:
       2 H / lone pairs
> center mol
The center is at: 4.92, -0.16, 17.45
> solvateCap mol TIP3PBOX {4.92, -0.16, 17.45} 10
Added 112 residues.
> saveAmberParm mol water_only.crd
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<WAT 208>.A<EP1 4> Could not find type: EP
For atom: .R<WAT 208>.A<EP2 5> Could not find type: EP
Parameter file was not saved.


I'd like to know what I can do to clear up above problem.

Thanks in advance.

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Received on Thu Jul 14 2005 - 11:53:00 PDT
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