AMBER Archive (2004)

Subject: AMBER: Use tleap convert *.pdb file to *.top and *.crd file

From: yonchen (yonchen_at_ic.sunysb.edu)
Date: Wed Mar 03 2004 - 22:01:04 CST

Dear Carsten and Case:

Thank you for your hints. I edited the original pdb file to make sure
that atom names are unique and I tried to create a frcmod as following
method.

antechamber -i bsheettest.pdb -fi pdb -o bsheettest.prep -fo prepi
parmchk -i bsheettest.prep -f prepi -o frcmod

But I still met the following problems.

[yongzhi_at_dhcp-143-109 exe]$ more frcmod
remark goes here
MASS

BOND

ANGLE

DIHE

IMPROPER
c3-c3-ca-ca 1.1 180.0 2.0 Using
default value
ca-ca-c3-ha 1.1 180.0 2.0 Using
default value
c3-ca-ca-ha 1.1 180.0 2.0 Using
default value
ca-ca-ca-ha 1.1 180.0 2.0 Using
default value
ca-ca-ca-oh 1.1 180.0 2.0 Using
default value
ca-ha-c3-na 1.1 180.0 2.0 Using
default value
c3-ca-na-ha 1.1 180.0 2.0 Using
default value
ca-ca-ca-na 1.1 180.0 2.0 Using
default value
ca-ca-ca-ca 1.1 180.0 2.0 Using
default value

NONBON

[yongzhi_at_dhcp-143-109 exe]$ tleap
-I: Adding /home/yongzhi/Documents/amber7/dat/leap/prep to search path.
-I: Adding /home/yongzhi/Documents/amber7/dat/leap/lib to search path.
-I: Adding /home/yongzhi/Documents/amber7/dat/leap/parm to search path.
-I: Adding /home/yongzhi/Documents/amber7/dat/leap/cmd to search path.

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
> loadamberparams frcmod
Loading parameters: ./frcmod
Reading force field mod type file (frcmod)
> bsheettest = loadpdb bsheettest.pdb
Loading PDB file: ./bsheettest.pdb
Created a new atom named: HNCA within residue: .R<NVAL 1>
Created a new atom named: H within residue: .R<NVAL 1>
Created a new atom named: HG11 within residue: .R<ILE 2>
Created a new atom named: HB1 within residue: .R<PHE 3>
Created a new atom named: HB1 within residue: .R<TYR 5>
Created a new atom named: HG11 within residue: .R<ILE 6>
Created a new atom named: HB1 within residue: .R<TRP 7>
Created a new atom named: HG11 within residue: .R<ILE 11>
Created a new atom named: HB1 within residue: .R<PHE 12>
Created a new atom named: HB1 within residue: .R<TYR 14>
Created a new atom named: HG11 within residue: .R<ILE 15>
Created a new atom named: HOCA within residue: .R<CVAL 16>
  total atoms in file: 295
  Leap added 12 missing atoms according to residue templates:
       12 H / lone pairs
  The file contained 12 atoms not in residue templates
  Since added/missing = extra, there is a high probability
  of atoms with 'incorrect' names; you may want to
  use addPdbAtomMap to map these names, or change in file
> saveamberparm bsheettest bsheettest.top bsheettest.crd
Checking Unit.
FATAL: Atom .R<NVAL 1>.A<HNCA 19> does not have a type.
FATAL: Atom .R<NVAL 1>.A<H 20> does not have a type.
FATAL: Atom .R<ILE 2>.A<HG11 20> does not have a type.
FATAL: Atom .R<PHE 3>.A<HB1 21> does not have a type.
FATAL: Atom .R<TYR 5>.A<HB1 22> does not have a type.
FATAL: Atom .R<ILE 6>.A<HG11 20> does not have a type.
FATAL: Atom .R<TRP 7>.A<HB1 25> does not have a type.
FATAL: Atom .R<ILE 11>.A<HG11 20> does not have a type.
FATAL: Atom .R<PHE 12>.A<HB1 21> does not have a type.
FATAL: Atom .R<TYR 14>.A<HB1 22> does not have a type.
FATAL: Atom .R<ILE 15>.A<HG11 20> does not have a type.
FATAL: Atom .R<CVAL 16>.A<HOCA 18> does not have a type.
Failed to generate parameters
Parameter file was not saved.

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