[gmx-users] adding metal-bonding parameters to a force field

Justin Lemkul jalemkul at vt.edu
Thu Apr 3 18:38:41 CEST 2014



On 4/3/14, 11:03 AM, Ahmet yıldırım wrote:
> Dear users,
>
> I renamed a water molecule' atoms bound to the Zn +2 ion in starting pdb. I
> get the following error by pdb2gmx (with -vsite hydrogens). How can I fix
> it?
> ..
> Making bonds...
> Number of bonds was 2, now 2
> Warning: cannot convert atom 3 HZ1 (bound to a heavy atom OZ with
>           2 bonds and 2 bound hydrogens atoms) to virtual site
>

It doesn't make sense to try to virtualize a water molecule.

-Justin

> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.5
>
>
>
>
> HOH:OWZ
> O:OZ
>
> XXX.pdb:
> ..
> HETATM 2068  OZ  OWZ A1001      -2.313  -0.628  16.011  1.00
> 8.54           O
> ...
>
> I modified as the following the some files.
>
> residuetypes.dat:
> OWZ    water ;modified
>
> aminoacids.hdb:
> OWZ    1 ;modified
> 2    7    HZ    OZ
>
> specbond.dat:
> ZN      ZN      1       OWZ     OZ      1       0.23    ZNOH2    ZOH2
> ;modified
>
> aminoacids.rtp:
> [ OWZ ];modified
>   [ atoms ]
>      OZ   OZ          -0.8824    0
>     HZ1   HZ           0.5001    0
>     HZ2   HZ           0.5001    0
>   [ bonds ]
>      OZ   HZ1
>      OZ   HZ2
>
> atomtypes.atp:
> OZ                16.00000    ; modified
> HZ                 1.00800    ; modified
>
> ffnonbonded.itp:
> OZ           8      16.00    0.0000  A   3.15061e-01  6.36386e-01
> ;modified
> HZ           1       1.008   0.0000  A   0.00000e+00  0.00000e+00
> ;modified
>
>
>
> 2014-04-02 16:35 GMT+03:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 4/2/14, 9:25 AM, Ahmet yıldırım wrote:
>>
>>> Dear Justin,
>>>
>>> I did as you said but I get the following error when I run grompp command.
>>> I don't know where is my mistake. What should I do to solve it?
>>>
>>> Fatal error:
>>> Too many warnings (1), grompp terminated.
>>> If you are sure all warnings are harmless, use the -maxwarn option.
>>>
>>> Please see tables from the link:
>>>
>>>
>> It's pointless for anyone to try to troubleshoot any of this without the
>> actual error produced by grompp.
>>
>> -Justin
>>
>>
>>   http://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source=
>>> web&cd=1&cad=rja&uact=8&ved=0CC0QFjAA&url=http%3A%2F%
>>> 2Fpubmedcentralcanada.ca%2Fpicrender.cgi%3Fartinstid%
>>> 3D1482211%26blobname%3DNIHMS61946-supplement-File002.pdf&ei=
>>> DGs6U560PMHxhQejyIDABg&usg=AFQjCNGUfMCQZYegoRpLGg5D9GjpFsPCxQ&sig2=vr6-
>>> 1syRClNsDmFdMlWyXw&bvm=bv.63934634,d.ZG4
>>>
>>>
>>> OH: the Zn-bound hydroxide oxygen atom when Zn-bound water is
>>> deprotonated,
>>> OW: Zn-bound water oxygen,
>>> NA and NB: the nitrogen atoms directly bound to the Zn +2 ion (NE2 (NB)
>>> atoms
>>> in His94 and His96, ND1 (NA) atom in His119).
>>>
>>>
>>> Table 1: specbond.dat:
>>> 14
>>> HIS     NA      1       ZN      ZN      1       0.205   HISD    ZNOH
>>> ;modified
>>> HIS     NB      1       ZN      ZN      1       0.205   HISE    ZNOH
>>> ;modified
>>> ZN      ZN      1       OH      OH      1       0.18    ZNOH    OH
>>> ;modified
>>> HIS     NA      1       ZN      ZN      1       0.205   HISD    ZNOH2
>>> ;modified
>>> HIS     NB      1       ZN      ZN      1       0.205   HISE    ZNOH2
>>> ;modified
>>> ZN      ZN      1       OW     OW      1       0.23    ZNOH2   HOH
>>> ;modified
>>>
>>>
>>> residuetypes.dat:
>>> ZNOH2    Ion ;modified
>>> ZNOH    Ion ;modified
>>>
>>>
>>> Table 2: aminoacids.rtp:
>>> [ ZNOH];modified
>>>    [ atoms ]
>>>     ZN      Zn           0.90920     1
>>> [ ZNOH2 ];modified
>>>    [ atoms ]
>>>     ZN      Zn           0.89230     1
>>>
>>>
>>> Table 1: ffnonbonded.itp:
>>> OW           8      16.00    0.0000  A   1.76820e-01  6.371092e-01
>>> ;modified
>>> Zn          30      65.4     0.0000  A   1.10000e-01  5.23250e-02
>>> ;modified
>>>
>>> Table 1: ffbonded.itp:
>>> [ bondtypes ]
>>>     ZN NA         1    0.20500   16744.00 ;modified
>>>     ZN NB         1    0.20500   16744.00 ;modified
>>>     ZN OH         1    0.18000   39348.40 ;modified
>>>     ZN OW         1    0.23000   16744.00 ;modified
>>>
>>> [ angletypes ]
>>> C   NA  ZN           1   126.0      83.720 ;modified
>>> C   NB  ZN           1   126.0      83.720 ;modified
>>> NA  ZN  NB           1   109.5      96.278 ;modified
>>> NB  ZN  NB           1   109.5      96.278 ;modified
>>> NA  ZN  OH           1   109.5      96.278 ;modified
>>> NB  ZN  OH           1   109.5      96.278 ;modified
>>> ZN  OH  HW           1   124.0      83.720 ;modified
>>> HW  OW  HW           1   104.5      4186.0 ;modified
>>>
>>> [ dihedraltypes ]
>>>    X   ZN  NA  X     9     0.000      0.00000     3  ;modified
>>>    X   ZN  NB  X     9     0.000      0.00000     3  ;modified
>>>    X   ZN  OH  X     9     0.000      0.00000     3  ;modified
>>>    X   ZN  OW  X     9     0.000      0.00000     3  ;modified
>>>
>>>
>>>
>>> 2014-04-01 16:05 GMT+03:00 Justin Lemkul <jalemkul at vt.edu>:
>>>
>>>
>>>>
>>>> On 4/1/14, 8:49 AM, Ahmet yıldırım wrote:
>>>>
>>>>   There are both Zn-OH(zinc-hydroxyl) and Zn-H2O (zinc-water) bond in
>>>>> structure, then should I modify "aminoacids.hdb" and "aminoacids.rtp" to
>>>>> add OH (hydroxyl) and water parameters?
>>>>>
>>>>>
>>>>>
>>>>>   The parameters listed in Table 1 need to be added to ffbonded.itp and
>>>> ffnonbonded.itp.  The thing to watch out for is that there are two
>>>> different H-O-H angles that are defined, depending on whether the water
>>>> is
>>>> free or bound to Zn.  Therefore, you need unique atomtypes to
>>>> differentiate
>>>> between different types of water, so that requires modification of
>>>> atomtypes.atp, as well, if you will be processing the structure with
>>>> pdb2gmx.
>>>>
>>>> Table 2 corresponds to a specific residue that needs to be added as an
>>>> .rtp entry (again, only if you are using pdb2gmx to create the topology).
>>>>    The .hdb entry is only necessary if you do not have H positions in the
>>>> input coordinate file.
>>>>
>>>> -Justin
>>>>
>>>>
>>>>    2014-04-01 11:03 GMT+03:00 Ahmet yıldırım <ahmedo047 at gmail.com>:
>>>>
>>>>>
>>>>>    Firstly, I will change ffnonbonded.itp and ffbonded.itp. Later?
>>>>>
>>>>>>
>>>>>>
>>>>>> 2014-04-01 10:37 GMT+03:00 Ahmet yıldırım <ahmedo047 at gmail.com>:
>>>>>>
>>>>>> Dear users,
>>>>>>
>>>>>>
>>>>>>> Please see the file from the link:
>>>>>>>
>>>>>>> http://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source=
>>>>>>> web&cd=1&cad=rja&uact=8&ved=0CC0QFjAA&url=http%3A%2F%
>>>>>>> 2Fpubmedcentralcanada.ca%2Fpicrender.cgi%3Fartinstid%
>>>>>>> 3D1482211%26blobname%3DNIHMS61946-supplement-File002.pdf&ei=
>>>>>>> DGs6U560PMHxhQejyIDABg&usg=AFQjCNGUfMCQZYegoRpLGg5D9GjpFs
>>>>>>> PCxQ&sig2=vr6-
>>>>>>> 1syRClNsDmFdMlWyXw&bvm=bv.63934634,d.ZG4
>>>>>>>
>>>>>>> I want to add table 1 and table 2 parameters to amber force field. How
>>>>>>> can
>>>>>>> I achieve it?
>>>>>>>
>>>>>>> --
>>>>>>> Ahmet Yıldırım
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Ahmet Yıldırım
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>   --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 601
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/
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>>>>
>>>>
>>>
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> 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
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>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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


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