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

[Roshan Shrestha]

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-

























































*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.*


-- 
Roshan Shrestha
Graduate Student
Central Department of Physics,Tribhuvan University
Kathmandu,Nepal