[gmx-users] adding metal-bonding parameters to a force field
Justin Lemkul
jalemkul at vt.edu
Fri Apr 4 15:31:03 CEST 2014
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
>>
>> * 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
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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
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