AMBER Archive (2004)

Subject: AMBER: How to use tleap convert *.pdb file to *.crd and *.top files

From: yonchen (yonchen_at_ic.sunysb.edu)
Date: Tue Mar 02 2004 - 13:08:55 CST

Dear Amber users,

I tried to use tleap to convert a simple pdb file to crd and top files.
It seems that tleap can not tell the items created by itself when the
pdb file was loaded. How to figure it out? The message are as
following.

Thanks a lot for the help.

Best wishes,
Yongzhi Chen

Welcome to LEaP!
(no leaprc in search path)
> source leaprc.ff99
----- Source: /home/yongzhi/Documents/amber7//dat/leap/cmd/leaprc.ff99
----- Source of
/home/yongzhi/Documents/amber7//dat/leap/cmd/leaprc.ff99
done
Log file: ./leap.log
Loading parameters:
/home/yongzhi/Documents/amber7//dat/leap/parm/parm99.dat
Loading library:
/home/yongzhi/Documents/amber7//dat/leap/lib/all_nucleic94.lib
Loading library:
/home/yongzhi/Documents/amber7//dat/leap/lib/all_amino94.lib
Loading library:
/home/yongzhi/Documents/amber7//dat/leap/lib/all_aminoct94.lib
Loading library:
/home/yongzhi/Documents/amber7//dat/leap/lib/all_aminont94.lib
Loading library:
/home/yongzhi/Documents/amber7//dat/leap/lib/ions94.lib
Loading library:
/home/yongzhi/Documents/amber7//dat/leap/lib/solvents.lib
> bsheet = loadpdb bsheet.pdb
Loading PDB file: ./bsheet.pdb
-- residue 1: duplicate [ HG1] atoms (total 3)
-- residue 1: duplicate [ HG2] atoms (total 3)
-- residue 2: duplicate [ HD1] atoms (total 3)
-- residue 2: duplicate [ HG1] atoms (total 2)
-- residue 2: duplicate [ HG2] atoms (total 3)
-- residue 4: duplicate [ HG1] atoms (total 3)
-- residue 4: duplicate [ HG2] atoms (total 3)
-- residue 6: duplicate [ HD1] atoms (total 3)
-- residue 6: duplicate [ HG1] atoms (total 2)
-- residue 6: duplicate [ HG2] atoms (total 3)
-- residue 8: duplicate [ HG1] atoms (total 3)
-- residue 8: duplicate [ HG2] atoms (total 3)
-- residue 9: duplicate [ HG2] atoms (total 3)
-- residue 10: duplicate [ HG1] atoms (total 3)
-- residue 10: duplicate [ HG2] atoms (total 3)
-- residue 11: duplicate [ HD1] atoms (total 3)
-- residue 11: duplicate [ HG1] atoms (total 2)
-- residue 11: duplicate [ HG2] atoms (total 3)
-- residue 13: duplicate [ HG1] atoms (total 3)
-- residue 13: duplicate [ HG2] atoms (total 3)
-- residue 15: duplicate [ HD1] atoms (total 3)
-- residue 15: duplicate [ HG1] atoms (total 2)
-- residue 15: duplicate [ HG2] atoms (total 3)
-- residue 16: duplicate [ HG1] atoms (total 3)
-- residue 16: duplicate [ HG2] atoms (total 3)

   ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (same-name atoms are reduced to a single atom)

Created a new atom named: HNC within residue: .R<NVAL 1>
Created a new atom named: H within residue: .R<NVAL 1>
Created a new atom named: HG2 within residue: .R<NVAL 1>
Created a new atom named: HG1 within residue: .R<NVAL 1>
Created a new atom named: HG2 within residue: .R<ILE 2>
Created a new atom named: HG1 within residue: .R<ILE 2>
Created a new atom named: HD1 within residue: .R<ILE 2>
Created a new atom named: HB1 within residue: .R<PHE 3>
Created a new atom named: HG2 within residue: .R<VAL 4>
Created a new atom named: HG1 within residue: .R<VAL 4>
Created a new atom named: HB1 within residue: .R<TYR 5>
Created a new atom named: HG2 within residue: .R<ILE 6>
Created a new atom named: HG1 within residue: .R<ILE 6>
Created a new atom named: HD1 within residue: .R<ILE 6>
Created a new atom named: HB1 within residue: .R<TRP 7>
Created a new atom named: HG2 within residue: .R<VAL 8>
Created a new atom named: HG1 within residue: .R<VAL 8>
Created a new atom named: HG2 within residue: .R<THR 9>
Created a new atom named: HG2 within residue: .R<VAL 10>
Created a new atom named: HG1 within residue: .R<VAL 10>
Created a new atom named: HG2 within residue: .R<ILE 11>
Created a new atom named: HG1 within residue: .R<ILE 11>
Created a new atom named: HD1 within residue: .R<ILE 11>
Created a new atom named: HB1 within residue: .R<PHE 12>
Created a new atom named: HG2 within residue: .R<VAL 13>
Created a new atom named: HG1 within residue: .R<VAL 13>
Created a new atom named: HB1 within residue: .R<TYR 14>
Created a new atom named: HG2 within residue: .R<ILE 15>
Created a new atom named: HG1 within residue: .R<ILE 15>
Created a new atom named: HD1 within residue: .R<ILE 15>
Created a new atom named: HG2 within residue: .R<CVAL 16>
Created a new atom named: HG1 within residue: .R<CVAL 16>
Created a new atom named: HOC within residue: .R<CVAL 16>
  total atoms in file: 295
  Leap added 79 missing atoms according to residue templates:
       79 H / lone pairs
  The file contained 33 atoms not in residue templates

> saveamberparm bsheet bsheet.top bsheet.crd
Checking Unit.
FATAL: Atom .R<NVAL 1>.A<HNC 19> does not have a type.
FATAL: Atom .R<NVAL 1>.A<H 20> does not have a type.
FATAL: Atom .R<NVAL 1>.A<HG2 21> does not have a type.
FATAL: Atom .R<NVAL 1>.A<HG1 22> does not have a type.
FATAL: Atom .R<ILE 2>.A<HG2 20> does not have a type.
FATAL: Atom .R<ILE 2>.A<HG1 21> does not have a type.
FATAL: Atom .R<ILE 2>.A<HD1 22> does not have a type.
FATAL: Atom .R<PHE 3>.A<HB1 21> does not have a type.
FATAL: Atom .R<VAL 4>.A<HG2 17> does not have a type.
FATAL: Atom .R<VAL 4>.A<HG1 18> does not have a type.
FATAL: Atom .R<TYR 5>.A<HB1 22> does not have a type.
FATAL: Atom .R<ILE 6>.A<HG2 20> does not have a type.
FATAL: Atom .R<ILE 6>.A<HG1 21> does not have a type.
FATAL: Atom .R<ILE 6>.A<HD1 22> does not have a type.
FATAL: Atom .R<TRP 7>.A<HB1 25> does not have a type.
FATAL: Atom .R<VAL 8>.A<HG2 17> does not have a type.
FATAL: Atom .R<VAL 8>.A<HG1 18> does not have a type.
FATAL: Atom .R<THR 9>.A<HG2 15> does not have a type.
FATAL: Atom .R<VAL 10>.A<HG2 17> does not have a type.
FATAL: Atom .R<VAL 10>.A<HG1 18> does not have a type.
FATAL: Atom .R<ILE 11>.A<HG2 20> does not have a type.
FATAL: Atom .R<ILE 11>.A<HG1 21> does not have a type.
FATAL: Atom .R<ILE 11>.A<HD1 22> does not have a type.
FATAL: Atom .R<PHE 12>.A<HB1 21> does not have a type.
FATAL: Atom .R<VAL 13>.A<HG2 17> does not have a type.
FATAL: Atom .R<VAL 13>.A<HG1 18> does not have a type.
FATAL: Atom .R<TYR 14>.A<HB1 22> does not have a type.
FATAL: Atom .R<ILE 15>.A<HG2 20> does not have a type.
FATAL: Atom .R<ILE 15>.A<HG1 21> does not have a type.
FATAL: Atom .R<ILE 15>.A<HD1 22> does not have a type.
FATAL: Atom .R<CVAL 16>.A<HG2 18> does not have a type.
FATAL: Atom .R<CVAL 16>.A<HG1 19> does not have a type.
FATAL: Atom .R<CVAL 16>.A<HOC 20> does not have a type.
Failed to generate parameters
Parameter file was not saved.

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