[gmx-users] my modified residue falls apart after MD
MD
refmac5 at gmail.com
Thu Nov 23 04:22:26 CET 2017
Yes. You are right about the names. I wrote them by memory and they were
not printed from the terminal. I will try to edit the ffbonded.itp and see
how it goes. Thanks!
Ming
On Wed, Nov 22, 2017 at 10:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/22/17 10:11 PM, MD wrote:
>
>> Justin, originally I did use SG and OE in the [bonds] and I got
>> complaints of "SG-OE no default bond type" "CB SG OE" no default U-B type
>> and "CT1, CT2, SG, OE" no default proper dihedral gypes. Are these the
>>
>
> Make sure you're clear on what needs to be done, because what you've
> written above is not correct and would never be printed - your dihedral is
> a mix of types and names. All parameters are assigned by type, never by
> name.
>
> parameters you mean that are missing? If so, what files do you think I
>> should modify to create these parameters? ffbonded.itp, merged.rtp and
>> residuetype.dat?
>>
>
> ffbonded.itp
>
>
> -Justin
>
> On Wed, Nov 22, 2017 at 10:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 11/22/17 9:57 PM, MD wrote:
>>>
>>> Thanks Justin. Then do I need to create new bond of SG and OE in
>>>> ffbonded.itp? Cause I have tried adding SG and OE bond in ffbonded.itp
>>>> and
>>>>
>>>> SG and OE are atom names, not types. That's not a valid approach.
>>>
>>> I got complaint from gromacs.. I modified the SG-OE bond from S-O bond
>>> and
>>>
>>>> it should work...
>>>>
>>>> The [bonds] section requires atom names in order to function, so use of
>>> SG
>>> and OE here is correct (your original entry used S and O, which are atom
>>> types and therefore not correct). If grompp subsequently complains about
>>> missing force field parameters when the correct bonds are written to the
>>> topology, then what you're attempting to do is not supported by the force
>>> field and you will have to either parametrize those missing interactions
>>> or
>>> find parameters.
>>>
>>> -Justin
>>>
>>>
>>> On Wed, Nov 22, 2017 at 9:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>>
>>>> On 11/22/17 9:32 PM, MD wrote:
>>>>>
>>>>> Hi gromacs folks,
>>>>>
>>>>>> I was trying to introduce sulfenic acid as modified cysteine to the
>>>>>> forcefield as following. Everything went well until the "gmx mdrun -v
>>>>>> -deffnm em". The only file I modified was merged.rtp since there were
>>>>>> no
>>>>>> new bond or dihedral angles. However my sulfenic acid falls apart
>>>>>> (oxygen
>>>>>> and sulfur are far away from the protein) after mdrun. Any help or
>>>>>> suggestions what I should do next? I am reading the manual at the same
>>>>>> time
>>>>>> but I thought maybe I can get some help here as well.
>>>>>>
>>>>>> Thank you for your time and any advice will be appreciated.
>>>>>>
>>>>>> Ming
>>>>>>
>>>>>> [ CSO ]
>>>>>> [ atoms ]
>>>>>> N NH1 -0.470 0
>>>>>> HN H 0.310 1
>>>>>> CA CT1 0.070 2
>>>>>> HA HB1 0.090 3
>>>>>> CB CT2 -0.110 4
>>>>>> HB1 HA2 0.090 5
>>>>>> HB2 HA2 0.090 6
>>>>>> SG S 0.6 7
>>>>>> OE O -0.83 8
>>>>>> HE1 H 0.160 9
>>>>>> C C 0.510 10
>>>>>> O O -0.510 11
>>>>>> [ bonds ]
>>>>>> CB CA
>>>>>> S CB
>>>>>> S O
>>>>>> N HN
>>>>>> N CA
>>>>>> C CA
>>>>>> C +N
>>>>>> CA HA
>>>>>> CB HB1
>>>>>> CB HB2
>>>>>> OE HE1
>>>>>> O C
>>>>>>
>>>>>> You need a bond between SG and OE.
>>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> 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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>>> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
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