[gmx-users] Using specbond.dat in pdb2gmx

Justin Lemkul jalemkul at vt.edu
Tue Jun 17 20:11:24 CEST 2014

On 6/17/14, 1:51 PM, Matthew Stancea wrote:
>>> 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?

No, absolutely not.  You should never modify the force field files in such a 
way.  The force field has expected nomenclature.  You must make your coordinate 
file match that nomenclature, not the other way around.  If you start removing 
atoms from the .rtp file, your whole setup will be junk.

The simple answer here has already been printed by pdb2gmx.  Use -ignh to have 
the H atoms built back onto the structure and magically named correctly.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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