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

Justin Lemkul jalemkul at vt.edu
Sun Nov 26 18:06:45 CET 2017 


On 11/26/17 11:13 AM, MD wrote:
> ​Thank you Justin.
>
> At the mean time I had another error after grompp, "ERROR 1 [file
> topol_Protein_chain_E.itp, line 52165]:
>    Unknown cmap torsion between atoms 3022 3024 3026 3046 3049"
>
> the 3022 3024 3026 3046 3049 in the itp files referred to the backbone
> (C-N-CA-C-N) of three connected residues R-W-T..

Double-check the atom types and make sure you haven't messed something 
up. Also note that your CSO residue needs a [cmap] directive like every 
other amino acid. If you've omitted it, add it.

> I looked at the backbone of the pdb and it looks alright. this error didn't

This isn't a problem with geometry, so the PDB tells you nothing.

> show up until today when i work from home using gromacs on another server.
> DO you think if this is caused by different versions?

No idea, but do the scientific thing and maintain consistency so you can 
eliminate variables.

-Justin

>
>
>
> On Sun, Nov 26, 2017 at 9:38 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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
>>>>>>>>>>
>>>>>>>>>> ==================================================
>>>>>>>>>>
>>>>>>>>>> --
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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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>>>>>> --
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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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>> * Please search the archive at http://www.gromacs.org/Support
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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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