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

[Berk Hess]

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 successfullySpecial Atom Distance matrix:                   HISE1   HISE2                   NE214   NE231

   HISE2   NE231   0.854   HISE3   NE248   0.751   0.847Start terminus: NH3+End terminus: COO-
-------------------------------------------------------

Program pdb2gmx, VERSION 4.5-beta3-dev-20100812-97d39Source 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 GROMACSwebsite 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<<



-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100824/18876060/attachment.html>