[gmx-users] pdb2gmx: intra-chain disulfide bond missing problem

[Justin Lemkul]

On 5/20/15 12:17 PM, Zhang, Cheng wrote:
> Dear GROMACS users,
>
> Can I ask a disulfide bond question if possible?
>
>
> The link below is my protein L50K.pdb with 5 disulfide bonds.
>
> https://copy.com/kPLlSianI4LtohNy
>
>
> After using
>
>
> gmx pdb2gmx -f L50K.pdb -o L50K_processed.gro -water spce -inter -ignh -merge interactive
>
>
> one of the disulfide bonds (i.e. Heavy Chain, HC 236-310) does not show up in the interactive prompt. As a result, they become -SH instead of -S-S- in the output .gro file (also in the link).
>
>
> I tried to search solutions but could not find the answer for this intra-chain disulfide bond missing problem. Could you please help me?
>
>
> Thank you very much.
>
>
> Yours sincerely
>
> Cheng
>
>
> (I was trying to upload the PDB file by attachment. But it seems that the mail has not been approved. So I use a link instead.)
>

The mailing list does not accept attachments.  What you did is correct.

The disulfide isn't formed because it does not meet the criteria in 
specbond.dat.  The two Cys SG are separated by 0.167 nm, which is outside of 
±10% of the 0.2 nm criterion in specbond.dat.  So either (1) change the value in 
specbond.dat to some intermediate value that will satisfy this disulfide and the 
others (in the ballpark of 0.185 nm) or (2) try minimizing (or maybe briefly 
simulating) the current structure with the current topology using a distance 
restraint to bring those two SG to a distance of 0.2 nm, then regenerate the 
topology.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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