[Dock-fans] Fwd: prepare_amber.pl problems

[Francesco Pietra]

As posted on the amber forum, module ambpdb in AmberTools 1.2 (used to
generate the pdb for amberscore) writes incorrectly the H atoms as
reported below. inprc/prmtop files, either created with Amber9 or
Amber10, give the correct atom names for LEU as first residue when
ambpdb from Amber9 is used.

Now I have two procedures that require resetting back to Amber9. The
one above, and creation of parameters for ligands with Antechamber (I
posrted earlier the last issue but no concern was triggered).

I'll check later if amberscore is now happy. It is supper time here in
Lucca. My Brittany has come to my office with unmistakable signs.

francesco


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Mon, Oct 13, 2008 at 6:17 PM
Subject: prepare_amber.pl problems
To: dock-fans <dock-fans at docking.org>


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