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

[Justin Lemkul]

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?

-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

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