[gmx-users] Creat a new residue.

[Justin Lemkul]

On 10/16/12 10:10 AM, spin wrote:
> 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!
>

Every residue needs its own .hdb entry if your coordinate file does not contain 
all the hydrogens.  Atoms named "O1" and "O2" get confused with terminal oxygen 
atoms.  Use different names and make sure you're not confusing types with names.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================