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

Sun Jan 21 17:21:01 CET 2018

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

>
> -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 <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
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> 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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