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

Ahmet yıldırım ahmedo047 at gmail.com
Fri Apr 4 19:46:56 CEST 2014


Dear Justin,

These parameters are present in literature. I think these bonds/parameters
are correctly generated. You said "The previous topology output suggests
not, because ZN is not renamed to ZNW".  I do not know what to do.

I added the OZ-HZ bond in ffbonded.itp. Unfortunately I get the same errors:

ERROR 1 [file protein_Ion_chain_A2.itp, line 33]:
  No default Bond types
ERROR 2 [file protein_Ion_chain_A2.itp, line 34]:
  No default Bond types

ffbonded.itp:
  Zn NA         1    0.20500   16744.0 ;modified
  Zn NB         1    0.20500   16744.0 ;modified
  Zn OZ         1    0.23000   16744.0 ;modified
  OZ HZ         1    0.09572   221682.2 ;modified


2014-04-04 16:29 GMT+03:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 4/4/14, 9:25 AM, Ahmet yıldırım wrote:
>
>> Dear Justin,
>>
>> Firstly, I renamed HETATM 2068  O  HOH A1001 in pdb. This water is bound
>> to
>> Zn.
>> its new name:
>> HETATM 2068  OZ  OWZ A1001
>>
>> Zn is bound to three Histidine atoms (two NE2 atoms and one ND1 atom) and
>> a
>> water molecule in carbonic anhydrase as I said before. I did the following
>> changes on amber99sb-ildn. What do you suggestion?
>>
>> specbond.dat:
>> 11
>> ..
>> HIS     ND1     1       ZN      Zn      1       0.205   HIDZ    ZNW
>> ;modified
>> HIS     NE2     1       ZN      Zn      1       0.205   HIEZ    ZNW
>> ;modified
>> OWZ     OZ      1       ZN      Zn      1       0.23    ZOH2    ZNW
>> ;modified
>>
>>
> Are these bonds correctly generated?  The previous topology output
> suggests not, because ZN is not renamed to ZNW.
>
>
>  residuetypes.dat:
>> ZNW    Ion   ;modified
>> ZOH2    water ;modified
>> OWZ    water ;modified
>> HIDZ    Protein
>> HIEZ    Protein
>>
>> aminoacids.hdb:
>> OWZ    1 ;modified
>> 2    7    HZ    OZ
>> ..
>> HIDZ    6
>> 1    1    H    N    -C    CA
>> 1    5    HA    CA    N    CB    C
>> 2    6    HB    CB    CA    CG
>> 1    1    HD1    ND1    CG    CE1
>> 1    1    HE1    CE1    ND1    NE2
>> 1    1    HD2    CD2    CG    NE2
>> HIEZ    6
>> 1    1    H    N    -C    CA
>> 1    5    HA    CA    N    CB    C
>> 2    6    HB    CB    CA    CG
>> 1    1    HE1    CE1    ND1    NE2
>> 1    1    HE2    NE2    CE1    CD2
>> 1    1    HD2    CD2    CG    NE2
>>
>> aminoacids.rtp:
>> [ ZNW ];modified
>>   [ atoms ]
>>     ZN     Zn           0.89230     1
>>
>> [ ZOH2 ];modified
>>   [ atoms ]
>>      OZ   OZ           -0.8824    0
>>     HZ1   HZ            0.5001    0
>>     HZ2   HZ            0.5001    0
>>   [ bonds ]
>>      OZ   HZ1
>>      OZ   HZ2
>>
>> [ OWZ ];modified
>>   [ atoms ]
>>      OZ   OZ           -0.8824    0
>>     HZ1   HZ            0.5001    0
>>     HZ2   HZ            0.5001    0
>>   [ bonds ]
>>      OZ   HZ1
>>      OZ   HZ2
>> [ HIDZ ];modified
>>   [ atoms ]
>>       N    N           -0.41570     1
>>       H    H            0.27190     2
>>      CA    CT           0.01880     3
>>      HA    H1           0.08810     4
>>      CB    CT          -0.04620     5
>>     HB1    HC           0.04020     6
>>     HB2    HC           0.04020     7
>>      CG    CC          -0.02660     8
>>     ND1    NA          -0.38110     9
>>     HD1    H            0.36490    10
>>     CE1    CR           0.20570    11
>>     HE1    H5           0.13920    12
>>     NE2    NB          -0.57270    13
>>     CD2    CV           0.12920    14
>>     HD2    H4           0.11470    15
>>       C    C            0.59730    16
>>       O    O           -0.56790    17
>>   [ bonds ]
>>       N     H
>>       N    CA
>>      CA    HA
>>      CA    CB
>>      CA     C
>>      CB   HB1
>>      CB   HB2
>>      CB    CG
>>      CG   ND1
>>      CG   CD2
>>     ND1   HD1
>>     ND1   CE1
>>     CE1   HE1
>>     CE1   NE2
>>     NE2   CD2
>>     CD2   HD2
>>       C     O
>>      -C     N
>>   [ impropers ]
>>      -C    CA     N     H
>>      CA    +N     C     O
>>      CG   CE1   ND1   HD1
>>      CG   NE2   CD2   HD2
>>     ND1   NE2   CE1   HE1
>>     ND1   CD2    CG    CB
>>
>> [ HIEZ ];modified
>>   [ atoms ]
>>       N    N           -0.41570     1
>>       H    H            0.27190     2
>>      CA    CT          -0.05810     3
>>      HA    H1           0.13600     4
>>      CB    CT          -0.00740     5
>>     HB1    HC           0.03670     6
>>     HB2    HC           0.03670     7
>>      CG    CC           0.18680     8
>>     ND1    NB          -0.54320     9
>>     CE1    CR           0.16350    10
>>     HE1    H5           0.14350    11
>>     NE2    NA          -0.27950    12
>>     HE2    H            0.33390    13
>>     CD2    CW          -0.22070    14
>>     HD2    H4           0.18620    15
>>       C    C            0.59730    16
>>       O    O           -0.56790    17
>>   [ bonds ]
>>       N     H
>>       N    CA
>>      CA    HA
>>      CA    CB
>>      CA     C
>>      CB   HB2
>>      CB   HB1
>>      CB    CG
>>      CG   ND1
>>      CG   CD2
>>     ND1   CE1
>>     CE1   HE1
>>     CE1   NE2
>>     NE2   HE2
>>     NE2   CD2
>>     CD2   HD2
>>       C     O
>>      -C     N
>>   [ impropers ]
>>      -C    CA     N     H
>>      CA    +N     C     O
>>     CE1   CD2   NE2   HE2
>>      CG   NE2   CD2   HD2
>>     ND1   NE2   CE1   HE1
>>     ND1   CD2    CG    CB
>>
>> atomtypes.atp:
>> OZ                16.00000    ; modified
>> HZ                 1.00800    ; modified
>>
>> ffbonded.itp:
>> [ bondtypes ]
>>    Zn NA         1    0.20500   16744.0 ;modified
>>    Zn NB         1    0.20500   16744.0 ;modified
>>    Zn OZ         1    0.23000   16744.0 ;modified
>>
>
> You get the fatal error about missing bond types because you haven't
> defined the OZ-HZ bond here.
>
> -Justin
>
>
>  [ angletypes ]
>> HW  OW  HW           1   104.5      142.490 ; TIP3P water ;modified
>>
>> CR  NA  Zn           1   126.0       83.720 ;modified
>> CW  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  OZ           1   109.5       96.278 ;modified
>> NB  Zn  OZ           1   109.5       96.278 ;modified
>> Zn  OZ  HZ           1   124.0       83.720 ;modified
>> HZ  OZ  HZ           1   104.5     4186.000 ;modified
>>
>> [ dihedraltypes ]
>>   X   Zn  NA  X     9       0.0      0.00000     3  ;modified
>>   X   Zn  NB  X     9       0.0      0.00000     3  ;modified
>>   X   Zn  OZ  X     9       0.0      0.00000     3  ;modified
>>
>> ffnonbonded.itp:
>> OW           8      16.00    0.0000  A   1.76820e-01  6.371092e-01
>> ;modified
>> 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
>> Zn          30      65.4     0.0000  A   1.10000e-01  5.23250e-02
>> ;modified
>>
>>
>> 2014-04-04 15:51 GMT+03:00 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>>>
>>> On 4/4/14, 8:47 AM, Ahmet yıldırım wrote:
>>>
>>>  Hi,
>>>>
>>>> The bond types are set properly in ffbonded.itp. But I get the following
>>>> errors after grompp command. How can I fix it?
>>>> ERROR 1 [file protein_Ion_chain_A2.itp, line 33]:
>>>>     No default Bond types
>>>>
>>>>
>>>> ERROR 2 [file protein_Ion_chain_A2.itp, line 34]:
>>>>     No default Bond types
>>>>
>>>> protein_Ion_chain_A2.itp:
>>>> [ moleculetype ]
>>>> ; Name            nrexcl
>>>> Ion_chain_A2        3
>>>>
>>>> [ atoms ]
>>>> ;   nr       type  resnr residue  atom   cgnr     charge       mass
>>>> typeB    chargeB      massB
>>>> ; residue 262 ZN  rtp ZN   q +2.0
>>>>        1         Zn    262     ZN     ZN      1          2       65.4
>>>> ;
>>>> qtot 2
>>>>
>>>>
>>> If I'm remembering your model right, the Zn-HOH complex doesn't bear a +2
>>> charge on Zn.  Is this what you actually want?
>>>
>>>
>>>   ; residue 1001 OWZ rtp OWZ  q +0.1
>>>
>>>>        2         OZ   1001    OWZ     OZ      2    -0.8824         16
>>>> ;
>>>> qtot 1.118
>>>>        3         HZ   1001    OWZ    HZ1      2     0.5001      1.008
>>>> ;
>>>> qtot 1.618
>>>>        4         HZ   1001    OWZ    HZ2      2     0.5001      1.008
>>>> ;
>>>> qtot 2.118
>>>>
>>>> [ bonds ]
>>>> ;  ai    aj funct            c0            c1            c2
>>>>  c3
>>>>       2     3     1
>>>>       2     4     1
>>>>
>>>>
>>>>  Apparently whatever ffbonded.itp file that is being read doesn't have
>>> these parameters.  Unfortunately, there's not enough information to say
>>> why.  If OZ-HZ parameters were there, there would be no reason they
>>> wouldn't be read.
>>>
>>> -Justin
>>>
>>>
>>>   [ angles ]
>>>
>>>> ;  ai    aj    ak funct            c0            c1
>>>> c2            c3
>>>>       3     2     4     1
>>>>
>>>> ; Include Position restraint file
>>>> #ifdef POSRES
>>>> #include "posre_Ion_chain_A2.itp"
>>>> #endif
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> 2014-04-04 0:32 GMT+03:00 Justin Lemkul <jalemkul at vt.edu>:
>>>>
>>>>
>>>>
>>>>> On 4/3/14, 2:58 PM, Gmail2 wrote:
>>>>>
>>>>>   Dear Justin,
>>>>>
>>>>>>
>>>>>> Zn bound to three Histidine atoms and a water in carbonic anhydrase.
>>>>>> This
>>>>>> water bound to Zn has different parameters than solvent water. That
>>>>>> parameters is present in literature. How should I set up such a
>>>>>> system?
>>>>>>
>>>>>> PS: I will use 'pdb2gmx' with -vsite hydrogens.
>>>>>>
>>>>>>
>>>>>>   If you need virtual sites, then you need to figure out how to
>>>>>> properly
>>>>>>
>>>>> build a virtual site database entry for that particular type of
>>>>> molecule.
>>>>>    That's entirely separate from any of the force field parameters
>>>>> you've
>>>>> shown before, but realize that doing so negates most of the Zn-HOH
>>>>> bonded
>>>>> parameters you posted.
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> 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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>>>>>
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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
>>>
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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!
>
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>
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>



-- 
Ahmet Yıldırım


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