[gmx-users] adding metal-bonding parameters to a force field
Ahmet yıldırım
ahmedo047 at gmail.com
Wed Apr 2 15:25:42 CEST 2014
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:
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=AFQjCNGUfMCQZYegoRpLGg5D9GjpFsPCxQ&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
>
> ==================================================
> --
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