[gmx-users] my modified residue falls apart after MD

Justin Lemkul jalemkul at vt.edu
Sun Nov 26 15:38:21 CET 2017 


On 11/26/17 9:32 AM, MD wrote:
> Thank you Mark.
>
> Do you think if the atom types of HE, OE and SG are correct in my
> merged.rtp? These are the three atoms which have name changing cause of the
> inserted sulfur. I modified their atom types as well. I need to make sure
> the type names are correct before I add the bond types in ffbonded.itp.

O is the carbonyl oxygen type in CHARMM, so I doubt that's a wise 
choice. You may also need an entirely different sulfur atom type. Have 
you assessed QM water interactions and dipole moments? Where did these 
charges come from? If you haven't done so already, you need to do some 
really basic validation before attempting to do anything with bonded 
parameters. The dihedrals will be particularly sensitive to the quality 
of LJ and charge terms.

-Justin

> [ 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
>     SG    CB
>     SG    OE
>      N    HN
>      N    CA
>      C    CA
>      C    +N
>     CA    HA
>     CB   HB1
>     CB   HB2
>             OE   HE1
>      O     C
>
>
> On Thu, Nov 23, 2017 at 12:25 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> You need to specify each bond you want, and for the types of those bonds to
>> have parameters available. Bonds are specified with atoms, bond types are
>> specified with atom types.
>>
>> Mark
>>
>> On Thu, 23 Nov 2017 04:22 MD <refmac5 at gmail.com> wrote:
>>
>>> 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 [bond​s] 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
>>>>>>> ff​bonded.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
>>>>>>>>
>>>>>>>> * 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
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> 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.
>>>>
>>> --
>>> 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.
>> --
>> 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

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

More information about the gromacs.org_gmx-users mailing list