[gmx-users] Using specbond.dat in pdb2gmx
jalemkul at vt.edu
Fri Jun 13 19:07:33 CEST 2014
On 6/13/14, 12:57 PM, Matthew Stancea wrote:
> Dr. Justin Lemkul,
> Now I understand the message about removal of bonds being just duplicate bonds that have been removed, and, also, I understand how the -ter flag works now.
>>> This is the screen output related to parsing of specbond.dat:
>>> "3 out of 3 lines of specbond.dat converted successfully
>>> Special Atom Distance matrix:
>>> CYS1 CYS1 CYS5 CYS5 VAL6 CYS10 CYS10
>>> N1 SG6 N47 SG52 C59 N101 SG106
>>> CYS1 SG6 0.302
>>> CYS5 N47 0.988 0.900
>>> CYS5 SG52 1.070 0.917 0.333
>>> VAL6 C59 1.498 1.396 0.510 0.585
>>> CYS10 N101 1.122 0.901 0.614 0.609 0.835
>>> CYS10 SG106 0.879 0.655 0.490 0.422 0.857 0.322
>>> CYS15 N160 0.784 0.488 1.066 0.984 1.477 0.774 0.620
>>> CYS15 SG165 0.477 0.202 0.960 0.961 1.432 0.823 0.625
>>> CYS17 N184 1.030 0.784 0.721 0.460 1.004 0.617 0.387
>>> CYS17 SG189 1.224 1.039 0.514 0.204 0.625 0.621 0.487
>>> VAL21 C245 0.756 0.685 0.408 0.388 0.847 0.812 0.531
>>> CYS22 N259 0.657 0.574 0.404 0.432 0.887 0.742 0.458
>>> CYS22 SG264 0.755 0.588 0.371 0.430 0.827 0.436 0.203
>>> VAL29 C363 0.132 0.394 1.117 1.193 1.626 1.248 1.004
>> Here is precisely why your specbond.dat is not working - the bond criteria are
>> not satisfied. The Cys1(N)-Val29(C) distance is 0.132 nm. You're specifing in
>> specbond.dat (likely from simply copying the contents of the other lines) that
>> the reference distance is 0.25 nm. If Gromacs does not find atoms within ±10%
>> of the value in specbond.dat, a bond won't be created. Since 0.132 nm is way
>> off, you won't get a bond.
>> Also note that your final columns will try to rename the residues to CYS2 (which
>> is specific for a disulfide cysteine, so unless that's true you'll get more
>> fatal errors) and VAL2, which doesn't exist.
>> See http://www.gromacs.org/Documentation/File_Formats/specbond.dat
> 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 ;)
> 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
> -Matthew Stancea
> (This email chain has gotten a bit long in my opinion, so I have put the previous email below. With your permission, I would prefer just using the above message in order to continue correspondence in shorter emails; however, if you would prefer to instead use the entire email, I completely understand.)
Snipping out relevant portions is perfectly fine (and preferred) as long as you
don't nuke something actually important.
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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