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

Justin Lemkul jalemkul at vt.edu
Sun Jan 21 17:33:28 CET 2018 


On 1/21/18 11:30 AM, MD wrote:
> 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?​

Is the image you showed before or after pdb2gmx? I'm trying to help you 
figure this out, but the information at hand is not consistent unless 
this structure is pre-pdb2gmx. What I was asking about was a structure 
*after* processing with pdb2gmx.

If pdb2gmx has converted these Cys to -SH form despite being told 
otherwise, please upload the original PDB file somewhere and provide a link.

-Justin

>>
>> -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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>>>>>>>> or
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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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>>>>>> * Please search the archive at http://www.gromacs.org/Support
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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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>>>> * Please search the archive at http://www.gromacs.org/Support
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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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>> * Please search the archive at http://www.gromacs.org/Support
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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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