[gmx-users] adding metal-bonding parameters to a force field
Ahmet yıldırım
ahmedo047 at gmail.com
Fri Apr 4 15:25:35 CEST 2014
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
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
[ 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
>>>
>>> * 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
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
--
Ahmet Yıldırım
More information about the gromacs.org_gmx-users
mailing list