[gmx-users] Using specbond.dat in pdb2gmx

Matthew Stancea mstancea at ggc.edu
Tue Jun 17 20:05:55 CEST 2014

>> Dr. Justin Lemkul,
>>>> Ah I see. I also noticed that in the original specbond.dat, the bond distance specification for the disulfide bonds between 2 CYS's or between 2 CYM's are .2 nm, not .25 nm, so I changed that as well. The only thing I still find a bit unclear is the final columns (residue rename). Is this what my specbond.dat file should look like?
>>> The final columns specify the new residue names that should be assigned to the
>>> residues only in the case that a special bond was created.  You'll see from the
>>> existing Cys specifications that a residue named "CYS" (standard PDB
>>> nomenclature for any Cys residue) is converted into the .rtp-specific CYS2, but
>>> only if a special bond is created.  The nomenclature exists because of the way
>>> the force fields work.  In your case, you don't need to rename anything, so
>>> preserving the original residue names is the proper way to go.

>>> Of course, the answer to "is this correct?" is generally obtained by running it ;)

>>>> 3
>>>> CYS     N       1       VAL     C       1       0.132    CYS    VAL
>>>> CYS     SG      1       CYS     SG      1       0.20    CYS2    CYS2
>>>> CYM     SG      1       CYM     SG      1       0.20    CYS2    CYS2

>> With the above specbond.dat file in the working directory, I attempted the command "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp" and received this fatal error message (it is the same as the original):

>> -------------------------------------------------------
>> Program pdb2gmx_mpi, VERSION 4.6.2
>> Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727
>> Fatal error:
>> Atom HB3 in residue CYS 1 was not found in rtp entry NCYX with 12 atoms
>> while sorting atoms.
>> For a hydrogen, this can be a different protonation state, or it
>> might 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.
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------

>Your input coordinate file does not conform to the required nomenclature of the
force field.  The error message says it all.

So according to the error message, it says that I can remove the HB3 from the rtp entry NCYX. I was able to locate that to at least one file: "residues.xml". 

Will editing that file (while backing up the original of course) allow me to bypass this error? For example, if I manually edit that file so that rtp entry NCYX contains all the atoms and only the atoms I want my initial atom to have, can pdb2gmx use that file in that way?

Thanks again!

-Matthew Stancea

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