[gmx-users] Creat a new residue.

[spin]

Hello, everyone,

I have created a new residue "CYM" in charmm27 force field. It consists of
the residue "CYS2" and MTSL which bonds to CYS2 by disulfide. The topology
of MTSL have been generated by CGenFF. I have added corresponding data to
aminoacid.rtp, ffbond.itp, ffnonbond.itp, atomtype.atp residuetypes,dat and
the protein's PDB file.  In the aminoacid.rtp, I have add all atoms'
topology information. 

Then I type the command:
 /pdb2gmx -f XX.pdb -o XX.gro -p XXtop -ss -his /

but it told me some atoms' missing:

/WARNING: atom HB2 is missing in residue CYM 90 in the pdb file
         You might need to add atom HB2 to the hydrogen database of building
block CYM
         in the file aminoacids.hdb (see the manual)


WARNING: atom O1 is missing in residue CYM 90 in the pdb file


WARNING: atom HN is missing in residue CYM 117 in the pdb file
         You might need to add atom HN to the hydrogen database of building
block CYM
         in the file aminoacids.hdb (see the manual)


WARNING: atom HA is missing in residue CYM 117 in the pdb file
         You might need to add atom HA to the hydrogen database of building
block CYM/
/         in the file aminoacids.hdb (see the manual)


WARNING: atom HB1 is missing in residue CYM 117 in the pdb file
         You might need to add atom HB1 to the hydrogen database of building
block CYM
         in the file aminoacids.hdb (see the manual)


WARNING: atom HB2 is missing in residue CYM 117 in the pdb file
         You might need to add atom HB2 to the hydrogen database of building
block CYM
         in the file aminoacids.hdb (see the manual)


WARNING: atom O1 is missing in residue CYM 117 in the pdb file


-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.4
Source code file: pdb2top.c, line: 1463

Fatal error:
There were 10 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology anyhow, use the option -missing
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors/

I checked the .hdb file, but it seemed not to require hydrogen adding for
CYS. Moreover, the atoms of MTSL like "O1" are not protein atoms, and they
are described by CGenFF. Now some of them are missing . Can you give me the
solution? Thank you!

Qing Liu



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