[Dock-fans] prepare_amber.pl problems

[Francesco Pietra]

I run into problems in trying to generate param/coord for an
amberscore simulation. Hydrogen names for LEU as first residue are
incorrect. The origin is from no-H pdb ambertools_1.2 leap (ambertools
1.2) to give prmtop inpcrd and then with ambpdb was obtained the pdb
that creates problems to prepare. LEU as residue 1, or as first
residue after a TER line:


ATOM      1  N   LEU     1
ATOM      2 1H   LEU     1
ATOM      3 2H   LEU     1
ATOM      4 2H   LEU     1
ATOM      5  CA  LEU     1
ATOM      6  HA  LEU     1
ATOM      7  CB  LEU     1
ATOM      8 2HB  LEU     1
ATOM      9 3HB  LEU     1
ATOM     10  CG  LEU     1
ATOM     11  HG  LEU     1
ATOM     12  CD1 LEU     1
ATOM     13 1HD1 LEU     1
ATOM     14 2HD1 LEU     1
ATOM     15 3HD1 LEU     1
ATOM     16  CD2 LEU     1
ATOM     17 1HD2 LEU     1
ATOM     18 2HD2 LEU     1
ATOM     19 3HD2 LEU     1
ATOM     20  C   LEU     1
ATOM     21  O   LEU     1


The log generated by the perl script "prepare_amber.pl" (which in
other cases worked OK in my hands) indicates that atom names are
incorrect, thus no prmtop/inpcrd are generated:



total atoms in file: 20179
  The file contained 3 atoms not in residue templates
>  z=combine { x flex_primary_scored.1 }
  Sequence:
  Sequence: FF1.inpcrd
>  savePdb z mod21_ASH_allHIP_vac_ambpdb.flex_primary_scored.1.amber.pdb
Writing pdb file: mod21_ASH_allHIP_vac_ambpdb.flex_primary_scored.1.amber.pdb
 Converting N-terminal residue name to PDB format: NLEU -> LEU
 Converting C-terminal residue name to PDB format: CLYS -> LYS
 Converting N-terminal residue name to PDB format: NLEU -> LEU
 Converting C-terminal residue name to PDB format: CLYS -> LYS
 Converting N-terminal residue name to PDB format: NLEU -> LEU
 Converting C-terminal residue name to PDB format: CTYR -> TYR
>  saveAmberParm z mod21_ASH_allHIP_vac_ambpdb.flex_primary_scored.1.prmtop mod21_ASH_allHIP_vac_ambpdb.flex_primary_scored.1.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -18.000200 is not zero.
FATAL:  Atom .R<NLEU 853>.A<H 22> does not have a type.
FATAL:  Atom .R<NLEU 428>.A<H 22> does not have a type.
FATAL:  Atom .R<NLEU 1>.A<H 22> does not have a type.
Failed to generate parameters
Parameter file was not saved.

I was tempted to remove LEU as first residue, but there might be a better way.

Thanks
francesco pietra