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Hi,<br><br>This was due to two simultaneous issues. I fixed them both for the next beta release.<br>Note that using HIS iso HISE as a residue name would solve the problem.<br>For 4.5 this should be the normal input, since residue names from the pdb are now preserved.<br><br>Berk<br><br><hr id="stopSpelling">From: alanwilter@gmail.com<br>Date: Mon, 23 Aug 2010 17:45:03 +0100<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] issue with pdb2gmx 4.5 and HISE oplsaa<br><br>Hi there,<div><br></div><div>I have a system with 'HISE' and using gmx 4.5.</div><div><br></div><div><div>ATOM 20 N HISE 2 6.376 3.718 -0.053 1.00 0.00 N </div><div>ATOM 21 H HISE 2 5.980 4.646 -0.135 1.00 0.00 H </div>
<div>ATOM 22 CA HISE 2 7.843 3.744 -0.109 1.00 0.00 C </div><div>ATOM 23 HA HISE 2 8.260 3.319 0.806 1.00 0.00 H </div><div>ATOM 24 CB HISE 2 8.319 2.925 -1.327 1.00 0.00 C </div>
<div>ATOM 25 HB2 HISE 2 7.855 1.940 -1.312 1.00 0.00 H </div><div>ATOM 26 HB1 HISE 2 7.985 3.435 -2.233 1.00 0.00 H </div><div>ATOM 27 CG HISE 2 9.807 2.703 -1.450 1.00 0.00 C </div>
<div>ATOM 28 ND1 HISE 2 10.461 2.463 -2.655 1.00 0.00 N </div><div>ATOM 29 CE1 HISE 2 11.770 2.542 -2.382 1.00 0.00 C </div><div>ATOM 30 HE1 HISE 2 12.557 2.484 -3.124 1.00 0.00 H </div>
<div>ATOM 31 NE2 HISE 2 11.969 2.794 -1.078 1.00 0.00 N </div><div>ATOM 32 HE2 HISE 2 12.817 3.173 -0.672 1.00 0.00 H </div><div>ATOM 33 CD2 HISE 2 10.740 2.839 -0.459 1.00 0.00 C </div>
<div>ATOM 34 HD2 HISE 2 10.579 3.098 0.574 1.00 0.00 H </div><div>ATOM 35 C HISE 2 8.279 5.228 -0.214 1.00 0.00 C </div><div>ATOM 36 O HISE 2 7.440 6.079 -0.525 1.00 0.00 O </div>
</div><div><br></div><div>when trying:</div><div><br></div><div>pdb2gmx -f oHHH.pdb -o ogHHH.pdb -p ogHHH.top -ff oplsaa -water none</div><div><br></div><div><div>Identified residue HISE1 as a starting terminus.</div><div>
Identified residue HISE3 as a ending terminus.</div><div>8 out of 8 lines of specbond.dat converted successfully</div><div>Special Atom Distance matrix:</div><div> HISE1 HISE2</div><div> NE214 NE231</div>
<div> HISE2 NE231 0.854</div><div> HISE3 NE248 0.751 0.847</div><div>Start terminus: NH3+</div><div>End terminus: COO-</div><div><br></div><div>-------------------------------------------------------</div><div>
Program pdb2gmx, VERSION 4.5-beta3-dev-20100812-97d39</div><div>Source code file: /Users/alan/Programmes/gromacs/src/kernel/pdb2gmx.c, line: 583</div><div><br></div><div>Fatal error:</div><div>Atom HE2 in residue HISE 1 not found in rtp entry HIS1 with 19 atoms</div>
<div>while sorting atoms. Maybe different protonation state.</div><div> Remove this hydrogen or choose a different protonation state.</div><div> Option -ignh will ignore all hydrogens in the input.</div>
<div>For more information and tips for troubleshooting, please check the GROMACS</div><div>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a></div><div><br></div>
Why error is referencing to HIS1 (= HISA = HISD in OPLS terminology, hence != HISE)</div><div><br></div><div>Many thanks in advance,</div><div><br></div><div>Alan<br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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