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

Sun Jan 21 17:06:04 CET 2018

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?

2. When you visualize the structure, both Cys335 and Cys338 are in their 
thiol (-SH) form?

-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
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>> --
>> ==================================================
>>
>> 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
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

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

==================================================