[gmx-users] Fractional charge for protein after topology preparation

[Agnivo Gosai]

Dear Users

I wanted to prepare the topology file for a particular protein system using
AMBER99SB through pdb2gmx, however I received numerous warnings and the
command crashed.

Hence I used the -missing tag with pdb2gmx to have a look at all the
warnings generated.
Typical warnings are given below :

1) WARNING: there were 0 atoms with zero occupancy and 8 atoms with
         occupancy unequal to one (out of 2569 atoms). Check your pdb file.

2) Warning: Long Bond (15-17 = 0.42516 nm)
Warning: Long Bond (15-17 = 0.42516 nm)

( above 30 such messages)

3)WARNING: atom CG is missing in residue GLN 17 in the pdb file


WARNING: atom HG1 is missing in residue GLN 17 in the pdb file
         You might need to add atom HG1 to the hydrogen database of
building block GLN
         in the file aminoacids.hdb (see the manual)


WARNING: atom HG2 is missing in residue GLN 17 in the pdb file
         You might need to add atom HG2 to the hydrogen database of
building block GLN
         in the file aminoacids.hdb (see the manual)


WARNING: atom CD is missing in residue GLN 17 in the pdb file


WARNING: atom OE1 is missing in residue GLN 17 in the pdb file


WARNING: atom NE2 is missing in residue GLN 17 in the pdb file


WARNING: atom HE21 is missing in residue GLN 17 in the pdb file
         You might need to add atom HE21 to the hydrogen database of
building block GLN
         in the file aminoacids.hdb (see the manual)

(Numerous !!)

4) WARNING: WARNING: Residue 2 named GLN of a molecule in the input file
was mapped
to an entry in the topology database, but the atom CD used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 8 named GLU of a molecule in the input file was
mapped
to an entry in the topology database, but the atom CG used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 25 named ARG of a molecule in the input file was
mapped
to an entry in the topology database, but the atom NE used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
 ( Again Numerous !!)

And lastly I get a fractional charge for the protein !!

Before cleaning: 6012 dihedrals
Keeping all generated dihedrals
Making cmap torsions...There are 6012 dihedrals,  434 impropers, 4106 angles
          5949 pairs,     2280 bonds and     0 virtual sites
Total mass 15942.450 a.m.u.
Total charge 3.336 e
Writing topology

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I looked at similar issues in the forum and I think that the PDB file I use
is corrupted and is a reason why I am getting "missing residue" warnings (
in sl. no. 3 and 4 of my mail).

However I am unable to understand the fractional charge for the protein.
Any suggestions ???


Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.