[gmx-users] adding metal-bonding parameters to a force field
Ahmet yıldırım
ahmedo047 at gmail.com
Thu Apr 3 17:03:23 CEST 2014
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
-------------------------------------------------------
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/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
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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.
>
--
Ahmet Yıldırım
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