AMBER Archive (2006)

Subject: AMBER: repeat use of a trimer lib file

From: Eric Hu (list.eric_at_gmail.com)
Date: Thu Jun 15 2006 - 18:35:39 CDT

Hi, I want to study the interaction of two trimers of a hexamer system
with Amber 8 in redhat linux. I build a trimer first with the monomer
ann.lib and ann.frcmod. Then I save the trimer lib file as tri.lib and
then read in a hexamer pdb file and hope to write out the crd and top
files where two trimers are distinguished. However it seems that the
tri.lib can not be used together with loadpdb command any more even
for the original tri.pdb file. So why is the tri.lib different from
the ann.lib file which can be used with loadpdb tri.pdb for the
trimer?

Thanks.
-Eric

The error message is like the following:

> loadoff tri.lib
Loading library: ./tri.lib
Loading: ann
> mod = loadamberparams ann.frcmod
Loading parameters: ./ann.frcmod
Reading force field mod type file (frcmod)
> ann = loadpdb tri.pdb
Loading PDB file: ./tri.pdb
Matching PDB residue names to LEaP variables.
(Residue 0: ann, Terminal/last, was not found in name map.)
(Residue 1: ann, Terminal/last, was not found in name map.)
(Residue 2: ann, Terminal/last, was not found in name map.)
  Added missing heavy atom: .R<ANN 2>.A<C01 1>
  Added missing heavy atom: .R<ANN 2>.A<C02 2>
  Added missing heavy atom: .R<ANN 2>.A<C03 3>
  Added missing heavy atom: .R<ANN 2>.A<C04 4>
  Added missing heavy atom: .R<ANN 2>.A<C05 5>
...
  Added missing heavy atom: .R<ANN 5>.A<N46 46>
  Added missing heavy atom: .R<ANN 5>.A<C27 27>
  Added missing heavy atom: .R<ANN 5>.A<N50 50>
  Added missing heavy atom: .R<ANN 5>.A<O55 55>
  total atoms in file: 165
  Leap added 330 missing atoms according to residue templates:
       240 Heavy
       90 H / lone pairs
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