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

MD refmac5 at gmail.com
Sun Jan 21 17:30:46 CET 2018 

On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/21/18 11:20 AM, MD wrote:
>
>> On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 1/21/18 10:59 AM, MD wrote:
>>>
>>> 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.​
>>>>
>>>> So, to be clear, please answer these two questions directly:
>>>
>>> 1. You find no line in [bonds] in topol_Protein_chain_B.itp file between
>>> atoms 2487 and 2507?
>>>
>>> ​Correct.​
>>
>>
>>
>> 2. When you visualize the structure, both Cys335 and Cys338 are in their
>>> thiol (-SH) form?
>>>
>> T
>> ​hey are not in thiol form. ​
>> ​
>> https://docs.google.com/document/d/1HOuMWAylWZOp1KP1cHRp82Y_
>> EiM5xAc8QM5KCAOOkSo/edit?usp=sharing
>> ​
>>
>
> This is not consistent with your above assertion. If your structure, after
> pdb2gmx or any point thereafter, does not have -SH, then you are modeling a
> disulfide. You can't simultaneously have no bond defined in the topology
> and also have no thiols. These are mutually exclusive. I suspect the bond
> was formed and you're perhaps looking in the wrong place.


​Then how can we explain there are no bond formed in the
topol_Protein_chain_B.itp?​

>
>
> -Justin
>
>
>
>>
>> -Justin
>>>
>>>
>>>
>>> -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
>>>>>>>> <https://maps.google.com/?q=n,+Jan+21,+2018+at+10:22+AM,+MD&entry=gmail&source=g>
>>>>>>>> <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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>>>>>
>>>>> --
>>> ==================================================
>>>
>>> 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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