[gmx-users] Using specbond.dat in pdb2gmx

[Mark Abraham]

ie. do the replacement on your input coordinate file, not the .rtp!


On Tue, Jun 17, 2014 at 10:35 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2
> and HB3 and use sed (or your text editor) to do the replacement.
>
> Mark
>
>
> On Tue, Jun 17, 2014 at 8:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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
>>
>> --
>> ==================================================
>>
>> 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
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>
>