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

[MD]

On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/21/18 10:46 AM, MD wrote:
>
>> 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
>>
>
> There is no indication that anything went wrong, and this should have been
> done. Are you saying that there is no line in the topology specifying a
> bond between atoms 2487 and 2507?


​Right. I didn't see anything said about the bond. I went forward to the
step of em.mdp and got a minimized gro, which was converted to pdb. And I
found no disulfide bond in the pdb file.​

>
>
> -Justin
>
>
> 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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>>>
> --
> ==================================================
>
> 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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> Gromacs Users mailing list
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