[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
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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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--
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