[gmx-users] Fw: Add new residue to oplsaa force field
Justin Lemkul
jalemkul at vt.edu
Wed Dec 17 13:58:20 CET 2014
On 12/17/14 3:50 AM, fatemeh ramezani wrote:
> Dear JustinThanks for your tip, After I edit atomtype in ffbonded file problem solved. There is a new problem. I made hydroxyprolin top file by mktop and I added bond, angle and dihedral parameters to the ffbonded file.
>
> ;
> ; This topology was generated by MKTOP ;
>
> ; Please cite this work.
>
> ; Ribeiro, A.A.S.T.; Horta, B.A.C.; de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7, 1433-1435, 2008.
>
> ; MKTOP does not generate charges!!! You will need to take care of that yourself!!
>
> ; Check your topology!! Make sure the atom types make sense.
>
> #include "/opt/bio/gromacs/share/gromacs/top/oplsaa.ff/forcefield.itp"
>
>
> [ moleculetype ]
> ; Name nrexcl
> MOL 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> 1 opls_902 1 HYP N1 5 -0.14000 14.0067
> 2 opls_135 1 HYP C1 1 0.01000 12.011
> 3 opls_235 1 HYP C2 2 0.50000 12.011
> 4 opls_281 1 HYP O1 2 -0.50000 15.9994
> 5 opls_136 1 HYP C3 3 -0.12000 12.011
> 6 opls_158 1 HYP C4 4 -0.12000 12.011
> 7 opls_908 1 HYP C5 5 -0.05000 12.011
> 8 opls_154 1 HYP O2 4 -0.68300 15.9994
> 9 opls_140 1 HYP H1 1 0.06000 1.008
> 10 opls_140 1 HYP H2 3 0.06000 1.008
> 11 opls_140 1 HYP H3 3 0.06000 1.008
> 12 opls_140 1 HYP H4 4 0.06000 1.008
> 13 opls_155 1 HYP H5 4 0.06000 1.008
> 14 opls_140 1 HYP H6 5 0.06000 1.008
> 15 opls_140 1 HYP H7 5 0.06000 1.008
>
> [ bonds ]
> 1 7 1 0.146 319657.6
> 1 2 1 0.147 319657.6
> 2 9 1 0.109 284512.0
> 2 5 1 0.154 224262.4
> 2 3 1 0.153 224262.4
> 3 4 1 0.122 200000.0
> 5 11 1 0.109 284512.0
> 5 10 1 0.109 284512.0
> 5 6 1 0.150 224262.4
> 6 12 1 0.109 284512.0
> 6 8 1 0.141 267776.0
> 6 7 1 0.151 224262.4
> 7 15 1 0.109 284512.0
> 7 14 1 0.109 284512.0
> 8 13 1 0.096 462750.4
>
>
> [ angles ]
> 1 7 6 1 103.026 470.281
> 1 7 15 1 113.597 292.880
> 1 7 14 1 109.458 292.880
> 1 2 9 1 114.712 292.880
> 1 2 5 1 103.936 470.281
> 1 2 3 1 108.272 669.440
> 2 1 7 1 110.799 433.462
> 2 5 11 1 113.386 313.800
> 2 5 10 1 109.493 313.800
> 2 5 6 1 103.337 488.273
> 2 3 4 1 120.399 200.000
> 3 2 9 1 106.795 418.400
> 3 2 5 1 112.252 585.760
> 5 2 9 1 110.968 313.800
> 5 6 12 1 113.836 313.800
> 5 6 8 1 108.872 418.400
> 5 6 7 1 103.268 488.273
> 6 5 11 1 113.403 313.800
> 6 5 10 1 109.458 313.800
> 6 8 13 1 109.466 460.240
> 6 7 15 1 113.577 313.800
> 6 7 14 1 109.490 313.800
> 7 6 12 1 113.170 313.800
> 7 6 8 1 109.597 418.400
> 8 6 12 1 107.964 292.880
> 10 5 11 1 107.676 276.144
> 14 7 15 1 107.597 276.144
>
>
> [ dihedrals ]
> 2 1 7 6 3
> 2 1 7 15 3
> 2 1 7 14 3
> 7 1 2 9 3
> 7 1 2 5 3
> 7 1 2 3 3
> 1 2 5 11 3
> 9 2 5 11 3
> 3 2 5 11 3
> 1 2 5 10 3
> 9 2 5 10 3
> 3 2 5 10 3
> 1 2 5 6 3
> 9 2 5 6 3
> 3 2 5 6 3
> 1 2 3 4 3
> 9 2 3 4 3
> 5 2 3 4 3
> 2 5 6 12 3
> 11 5 6 12 3
> 10 5 6 12 3
> 2 5 6 8 3
> 11 5 6 8 3
> 10 5 6 8 3
> 2 5 6 7 3
> 11 5 6 7 3
> 10 5 6 7 3
> 5 6 8 13 3
> 12 6 8 13 3
> 7 6 8 13 3
> 5 6 7 1 3
> 12 6 7 1 3
> 8 6 7 1 3
> 5 6 7 15 3
> 12 6 7 15 3
> 8 6 7 15 3
> 5 6 7 14 3
> 12 6 7 14 3
> 8 6 7 14 3
>
>
> [ dihedrals ]
>
>
> [ pairs ]
> 6 2 1
> 15 2 1
> 14 2 1
> 9 7 1
> 5 7 1
> 3 7 1
> 11 1 1
> 11 9 1
> 11 3 1
> 10 1 1
> 10 9 1
> 10 3 1
> 6 1 1
> 6 9 1
> 6 3 1
> 4 1 1
> 4 9 1
> 4 5 1
> 12 2 1
> 12 11 1
> 12 10 1
> 8 2 1
> 8 11 1
> 8 10 1
> 7 2 1
> 7 11 1
> 7 10 1
> 13 5 1
> 13 12 1
> 13 7 1
> 1 5 1
> 1 12 1
> 1 8 1
> 15 5 1
> 15 12 1
> 15 8 1
> 14 5 1
> 14 12 1
> 14 8 1
>
>
> [ system ]
> ; Name
> MKTOP
>
> [ molecules ]
> ; Compound #mols
> MOL 1
> As you can see in the topology file from mktop, there is no dihedral coefficients in the proper dihedral section that leads to creation of new error after grompp command. Why mktop doesn't produce these dihedral coefficient? and how can I solve it?Thanks in advance
>
Coefficients don't appear in the .top (except for Gromos force fields, because
they work a little differently). They are looked up from ffbonded.itp when
grompp is invoked.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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