[gmx-users] Fatal Error while using CHARMM 36 force field

[Justin Lemkul]

On 10/4/16 6:02 AM, Roshan Shrestha wrote:
> I mutated a peptide from Valine to Isoleucine and ran pdb2gmx command using
> CHARMM force field, however a fatal error occurred like this-
>
>
>
> *Atom HG in residue SER 15 was not found in rtp entry SER with 11
> atomswhile sorting atoms.*
> The whole output on the screen look like this-
 >

When renaming your atoms, you were probably overzealous.  Changing Val to Ile 
should not touch Ser, but clearly it did (and therefore you may have other 
problems elsewhere).  The error message tells you what to do; rename the H 
appropriately or use -ignh.  Refer to the .rtp file for the correct atom name.

-Justin

> *Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-jun2015.ff/merged.r2bReading
> mut.pdb...Read 378 atomsAnalyzing pdb fileSplitting chemical chains based
> on TER records or chain id changing.There are 1 chains and 0 blocks of
> water and 40 residues with 378 atoms  chain  #res #atoms  1 'A'    40
> 378  All occupancies are oneOpening force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-jun2015.ff/atomtypes.atpAtomtype
> 384Reading residue database... (charmm36-jun2015)Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-jun2015.ff/merged.rtpResidue
> 699Sorting it all out...Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-jun2015.ff/merged.hdbOpening
> force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-jun2015.ff/merged.n.tdbOpening
> force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-jun2015.ff/merged.c.tdbProcessing
> chain 1 'A' (378 atoms, 40 residues)Analysing hydrogen-bonding network for
> automated assignment of histidine protonation. 59 donors and 65 acceptors
> were found.There are 78 hydrogen bondsWill use HISE for residue 11Will use
> HISE for residue 28Will use HISE for residue 35Will use HISE for residue
> 36Identified residue ALA1 as a starting terminus.Identified residue ILE40
> as a ending terminus.8 out of 8 lines of specbond.dat converted
> successfullySpecial Atom Distance matrix:                    MET2   CYS10
> HIS11   CYS21   HIS28   HIS35                    SD15    SG78   NE290
> SG179  NE2255  NE2322   CYS10    SG78   1.382   HIS11   NE290   2.209
> 0.878   CYS21   SG179   1.461   1.284   1.895   HIS28  NE2255   1.768
> 2.223   2.812   1.158   HIS35  NE2322   3.189   3.031   3.173   2.162
> 1.688   HIS36  NE2334   2.948   2.942   3.211   1.929   1.316   0.475Start
> terminus ALA-1: NH3+End terminus ILE-40: COO-Opening force field file
> /usr/local/gromacs/share/gromacs/top/charmm36-jun2015.ff/merged.arn-------------------------------------------------------Program
> gmx pdb2gmx, VERSION 5.1.3Source code file:
> /home/rajendra/Desktop/gromacs-5.1.3/src/gromacs/gmxpreprocess/pdb2gmx.c,
> line: 746Fatal error:Atom HG in residue SER 15 was not found in rtp entry
> SER with 11 atomswhile sorting atoms.For a hydrogen, this can be a
> different protonation state, or itmight have had a different number in the
> PDB file and was rebuilt(it might for instance have been H3, and we only
> expected H1 & H2).Note that hydrogens might have been added to the entry
> for the N-terminus.Remove this hydrogen or choose a different protonation
> state to solve it.Option -ignh will ignore all hydrogens in the input.*
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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