AMBER Archive (2004)

Subject: AMBER: paramitrization problem

From: lei jia (jial_at_broyde.nyu.edu)
Date: Mon Jun 07 2004 - 17:12:37 CDT

Dear Amber Users,

I am trying to paramitrize the force field (Amber7) for a special
molecule. I added more than 10 new atom types, and bond lengths, bond
angles, dihedral angles, impropers and vdw parameters corresponding to
new atom types in the Parm99.dat. Then I added new atom types in the
leaprc file. I had no problem to run xLeap and load my new molecule in
with a Prep file. No parameters were missing But when I use 'solvatebox'
to add water in the system. It can't give me the right radius for each
atom.Instead, I got the warnings like this:

> solvatebox a WATBOX216 2.0
  (using default radius 1.500000 for O3')
 (using default radius 1.500000 for C2')
 (using default radius 1.500000 for C3')
 (using default radius 1.500000 for O2)
 (using default radius 1.500000 for C2)
 (using default radius 1.500000 for N3)
 (using default radius 1.500000 for N4)
 (using default radius 1.500000 for C4)
 (using default radius 1.500000 for C5)
 (using default radius 1.500000 for C6)
 (using default radius 1.500000 for N1)
 (using default radius 1.500000 for C1')
 (using default radius 1.500000 for O4')
 (using default radius 1.500000 for C4')
 (using default radius 1.500000 for C5')
 (using default radius 1.500000 for O5')
 (using default radius 1.500000 for O3')
 (using default radius 1.500000 for O6)
 (using default radius 1.500000 for C6)
 (using default radius 1.500000 for N1)
 (using default radius 1.500000 for N2)
 (using default radius 1.500000 for C2)
 (using default radius 1.500000 for N3)
 (using default radius 1.500000 for C4)
 (using default radius 1.500000 for O5)
 (using default radius 1.500000 for C5)
 (using default radius 1.500000 for N7)
 (using default radius 1.500000 for O8)
 (using default radius 1.500000 for C8)
 (using default radius 1.500000 for N9)
....

But actually Leap did add water in my system. When I tried to use
'saveAmberParm' to generate the topology file,it gave me such warnings:

Building topology.
Building atom parameters.
For atom: .R<DC5 5>.A<H5T 1> Could not find type: HO
For atom: .R<DC5 5>.A<O5' 2> Could not find type: OH
For atom: .R<DC5 5>.A<C5' 3> Could not find type: CT
For atom: .R<DC5 5>.A<H5'1 4> Could not find type: H1
For atom: .R<DC5 5>.A<H5'2 5> Could not find type: H1
For atom: .R<DC5 5>.A<C4' 6> Could not find type: CT
For atom: .R<DC5 5>.A<H4' 7> Could not find type: H1
For atom: .R<DC5 5>.A<O4' 8> Could not find type: OS
For atom: .R<DC5 5>.A<C1' 9> Could not find type: CT
For atom: .R<DC5 5>.A<H1' 10> Could not find type: H2
For atom: .R<DC5 5>.A<N1 11> Could not find type: N*
For atom: .R<DC5 5>.A<C6 12> Could not find type: CM
For atom: .R<DC5 5>.A<H6 13> Could not find type: H4
For atom: .R<DC5 5>.A<C5 14> Could not find type: CM
For atom: .R<DC5 5>.A<H5 15> Could not find type: HA
For atom: .R<DC5 5>.A<C4 16> Could not find type: CA
For atom: .R<DC5 5>.A<N4 17> Could not find type: N2
For atom: .R<DC5 5>.A<H41 18> Could not find type: H
For atom: .R<DC5 5>.A<H42 19> Could not find type: H
For atom: .R<DC5 5>.A<N3 20> Could not find type: NC
For atom: .R<DC5 5>.A<O2 22> Could not find type: O
For atom: .R<DC5 5>.A<C3' 23> Could not find type: CT
For atom: .R<DC5 5>.A<H3' 24> Could not find type: H1
.....

It looks like the original atom types were not recognized. And topology
file was not saved.Does anyone have experiences to parametrize the force
field and tell me how to figure my problems out?I appreciate any
suggestions.

Lei Jia

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