[gmx-users] disulfide bond missing even with -ss

[MD]

On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/21/18 10:29 AM, MD wrote:
>
>> I modified the specbond.dat and change the cutoff to be 2.04A, still
>> nothing...
>>
>
> Please don't spam the list with minute-by-minute updates.
>

​
sorry
​for the scattered information, ​
I didn't mean to spam the thread..



> Provide your pdb2gmx command, full screen output, and whatever evidence
> you have that the bond wasn't formed. The definitive answer is in your
> topology. If it's not there, we can diagnose.
>

​
command line: gmx pdb2gmx -f ncat.pdb -o ncat.gro -water spc -ignh -ss



Link CYS-335 SG-2487 and CYS-338 SG-2507 (y/n) ?y
Start terminus THR-24: NH3+
End terminus LEU-385: COO-
Opening force field file ./charmm36-jul2017.ff/merged.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 362 residues with 5724 atoms
Chain time...

Back Off! I just backed up topol_Protein_chain_B.itp to
./#topol_Protein_chain_B.itp.5#
Making bonds...
Warning: Long Bond (3206-3204 = 0.339276 nm)
Number of bonds was 5800, now 5800
Generating angles, dihedrals and pairs...
Before cleaning: 15256 pairs
Before cleaning: 15446 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are  359 cmap torsion pairs
There are 15446 dihedrals,  949 impropers, 10509 angles
          15142 pairs,     5800 bonds and     0 virtual sites
Total mass 40928.695 a.m.u.
Total charge -13.000 e
Writing topology

Back Off! I just backed up posre_Protein_chain_B.itp to
./#posre_Protein_chain_B.itp.5#
Processing chain 2 'B' (1 atoms, 1 residues)
Warning: Starting residue MG430 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file ./charmm36-jul2017.ff/merged.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 1 atoms
Chain time...

Back Off! I just backed up topol_Ion_chain_B2.itp to
./#topol_Ion_chain_B2.itp.5#
Making bonds...
No bonds
Generating angles, dihedrals and pairs...
Making cmap torsions...
There are    0 dihedrals,    0 impropers,    0 angles
             0 pairs,        0 bonds and     0 virtual sites
Total mass 24.305 a.m.u.
Total charge 2.000 e
Writing topology

Back Off! I just backed up posre_Ion_chain_B2.itp to
./#posre_Ion_chain_B2.itp.5#
Including chain 1 in system: 5724 atoms 362 residues
Including chain 2 in system: 1 atoms 1 residues
Now there are 5725 atoms and 363 residues
Total mass in system 40953.000 a.m.u.
Total charge in system -11.000 e

Writing coordinate file...

Back Off! I just backed up ncat.gro to ./#ncat.gro.5#



https://docs.google.com/document/d/1HOuMWAylWZOp1KP1cHRp82Y_EiM5xAc8QM5KCAOOkSo/edit?usp=sharing
​
 ​


>
> -Justin
>
> On Sun, Jan 21, 2018 at 10:23 AM, MD <refmac5 at gmail.com> wrote:
>>
>> I have also tried renaming my two CYS to be CYS2 but no luck either.
>>>
>>> On Sun, Jan 21, 2018 at 10:22 AM, MD <refmac5 at gmail.com> wrote:
>>>
>>> gromacs did ask me to confirm linking the two cys before the run, but I
>>>> didn't see any log saying the bond is formed.
>>>>
>>>> On Sun, Jan 21, 2018 at 10:19 AM, MD <refmac5 at gmail.com> wrote:
>>>>
>>>> Hi Gromacs folks,
>>>>> I realized I kept losing disulfide bond after gmx. The length is 2.01A
>>>>> but I did use -ss when pdb2gmx. Any thoughts?
>>>>> Thanks,
>>>>> Ming
>>>>>
>>>>>
>>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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