[gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa

[Alan]

Hi there,

I have a system with 'HISE' and using gmx 4.5.

ATOM     20  N   HISE    2       6.376   3.718  -0.053  1.00  0.00
N
ATOM     21  H   HISE    2       5.980   4.646  -0.135  1.00  0.00
H
ATOM     22  CA  HISE    2       7.843   3.744  -0.109  1.00  0.00
C
ATOM     23  HA  HISE    2       8.260   3.319   0.806  1.00  0.00
H
ATOM     24  CB  HISE    2       8.319   2.925  -1.327  1.00  0.00
C
ATOM     25  HB2 HISE    2       7.855   1.940  -1.312  1.00  0.00
H
ATOM     26  HB1 HISE    2       7.985   3.435  -2.233  1.00  0.00
H
ATOM     27  CG  HISE    2       9.807   2.703  -1.450  1.00  0.00
C
ATOM     28  ND1 HISE    2      10.461   2.463  -2.655  1.00  0.00
N
ATOM     29  CE1 HISE    2      11.770   2.542  -2.382  1.00  0.00
C
ATOM     30  HE1 HISE    2      12.557   2.484  -3.124  1.00  0.00
H
ATOM     31  NE2 HISE    2      11.969   2.794  -1.078  1.00  0.00
N
ATOM     32  HE2 HISE    2      12.817   3.173  -0.672  1.00  0.00
H
ATOM     33  CD2 HISE    2      10.740   2.839  -0.459  1.00  0.00
C
ATOM     34  HD2 HISE    2      10.579   3.098   0.574  1.00  0.00
H
ATOM     35  C   HISE    2       8.279   5.228  -0.214  1.00  0.00
C
ATOM     36  O   HISE    2       7.440   6.079  -0.525  1.00  0.00
O

when trying:

pdb2gmx -f oHHH.pdb -o ogHHH.pdb -p ogHHH.top -ff oplsaa -water none

Identified residue HISE1 as a starting terminus.
Identified residue HISE3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                   HISE1   HISE2
                   NE214   NE231
   HISE2   NE231   0.854
   HISE3   NE248   0.751   0.847
Start terminus: NH3+
End terminus: COO-

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5-beta3-dev-20100812-97d39
Source code file: /Users/alan/Programmes/gromacs/src/kernel/pdb2gmx.c, line:
583

Fatal error:
Atom HE2 in residue HISE 1 not found in rtp entry HIS1 with 19 atoms
while sorting atoms. Maybe different protonation state.
             Remove this hydrogen or choose a different protonation state.
             Option -ignh will ignore all hydrogens in the input.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Why error is referencing to HIS1 (= HISA = HISD in OPLS terminology, hence
!= HISE)

Many thanks in advance,

Alan
-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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