[gmx-users] adding metal-bonding parameters to a force field
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ahmedo047 at gmail.com
Thu Apr 3 20:58:55 CEST 2014
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.
Thanks in advance
Ahmet Yıldırım
3 Nis 2014 tarihinde 19:36 saatinde, Justin Lemkul <jalemkul at vt.edu> şunları yazdı:
>
>
>> 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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>>>>> 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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
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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
>
> ==================================================
> --
> 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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