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

[Alan]

Thanks Berk, it seems to be working now.

Alan

On 24 August 2010 08:54, Berk Hess <gmx3 at hotmail.com> wrote:

>  Hi,
>
> This was due to two simultaneous issues. I fixed them both for the next
> beta release.
> Note that using HIS iso HISE as a residue name would solve the problem.
> For 4.5 this should be the normal input, since residue names from the pdb
> are now preserved.
>
> Berk
>
> ------------------------------
> From: alanwilter at gmail.com
> Date: Mon, 23 Aug 2010 17:45:03 +0100
>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa
>
>
> 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 <http://www.bio.cam.ac.uk/%7Eawd28><<
>
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-- 
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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