May I ask how to set the hydrogens for LEU as first residue?
The inpcrd and prmtop, or pdb (generated with LEaP [ambertool 1.2] and
ambpdb from
no-hydrogens pdb), opens correctly in Chimera. For LEU as residue 1
(or as first residue after a TER line) reads:
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.
Thanks
francesco pietra
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Received on Wed Oct 15 2008 - 05:07:51 PDT
