[gmx-users] Add new residue to forcefield
Justin Lemkul
jalemkul at vt.edu
Tue Dec 16 13:47:12 CET 2014
On 12/16/14 4:53 AM, fatemeh ramezani wrote:
> Hi Dear gmx-users
> I want to simulate a tripeptide contain hydroxyprolin by OPLSAA. I added hydroxyprolin parameters as
> follow:
>
> in .hdb file :
>
> HYP 5
> 1 5 HA CA N C CB
> 2 6 HB CB CG CA
> 1 6 HG CG CD CB
> 1 6 HD CD N CG
> 1 4 HO OH CG CD
>
>
> in aminoacids.c.tdb file:
> [ HYP-COO- ]
> [ replace ]
> CA CA opls_285 12.011 -0.09
> C C opls_271 12.011 0.7
> O O1 opls_272 15.9994 -0.8
> OXT O2 opls_272 15.9994 -0.8
> [ add ]
> 2 8 O C CA N
> opls_272 15.9994 -0.8
> [ impropers ]
> CA O1 C O2 improper_O_C_X_Y
>
> [ HYP-ZWITTERION_COO- ]
> [ replace ]
> CA CA opls_246 12.011 0.13
> C C opls_271 12.011 0.7
> O O1 opls_272 15.9994 -0.8
> OXT O2 opls_272 15.9994 -0.8
> [ add ]
> 2 8 O C CA N
> opls_272 15.9994 -0.8
> [ impropers ]
> CA O1 C O2 improper_O_C_X_Y
>
>
>
> in aminoacids.n.tdb file:
>
Looks like you copied the .c.tdb entries instead of .n.tdb, as these would not
function as N-terminal patches.
> [ HYP-COO- ]
> [ replace ]
> CA CA opls_285 12.011 -0.09
> C C opls_271 12.011 0.7
> O O1 opls_272 15.9994 -0.8
> OXT O2 opls_272 15.9994 -0.8
> [ add ]
> 2 8 O C CA N
> opls_272 15.9994 -0.8
> [ impropers ]
> CA O1 C O2 improper_O_C_X_Y
>
> [ HYP-ZWITTERION_COO- ]
> [ replace ]
> CA CA opls_246 12.011 0.13
> C C opls_271 12.011 0.7
> O O1 opls_272 15.9994 -0.8
> OXT O2 opls_272 15.9994 -0.8
> [ add ]
> 2 8 O C CA N
> opls_272 15.9994 -0.8
> [ impropers ]
> CA O1 C O2 improper_O_C_X_Y
>
>
> in aminoacids.rtp file:
> [HYP]
> [ atoms ]
> N opls_239 -0.140 1
> CA opls_246 0.010 1
> HA opls_140 0.060 1
> CB opls_136 -0.120 2
> HB1 opls_140 0.060 2
> HB2 opls_140 0.060 2
> CG opls_136 -0.120 3
> HG1 opls_140 0.060 3
> OH opls_167 -0.683 3
> HO opls_168 0.435 3
> CD opls_245 -0.050 4
> HD1 opls_140 0.060 4
> HD2 opls_140 0.060 4
> C opls_235 0.500 5
> O opls_236 -0.500 5
> [ bonds ]
> N CA
> CA HA
> CA CB
> CA C
> CB HB1
> CB HB2
> CB CG
> CG HG1
> CG OH
> OH HO
> CG CD
> CD HD1
> CD HD2
> CD N
> C O
> -C N
> [ impropers ]
> -C CA N CD improper_Z_N_X_Y
> CA +N C O improper_O_C_X_Y
>
> in ffbonded.itp file:
>
> [ bondtypes ]
> CG OH 2 0.144 6100000.0 ;
> OH HO 2 0.100 15700000.0 ;
>
>
> [ angletypes ]
> ; i j k func th0 cth
> CG CB OH 2 109.5 520.0
> OH CG CD 2 109.5 520.0
> CG OH HO 2 109.5 450.0
>
> [ dihedraltypes ]
> CG CB CD OH 1 35.3 334.8
> CB CG OH HO 1 0.0 1.3 3
>
>
> After pdb2gmx command top file was generated:
> ...
> ; Include forcefield parameters
> #include "./oplsaa.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Protein 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
> ; residue 22 PRO rtp PRO q +0.9
> 1 opls_309 22 PRO N 1 -0.2 14.0067 ; qtot -0.2
> 2 opls_310 22 PRO H1 1 0.31 1.008 ; qtot 0.11
> 3 opls_310 22 PRO H2 1 0.31 1.008 ; qtot 0.42
> 4 opls_246 22 PRO CA 1 0.13 12.011 ; qtot 0.55
> 5 opls_140 22 PRO HA 1 0.06 1.008 ; qtot 0.61
> 6 opls_136 22 PRO CB 2 -0.12 12.011 ; qtot 0.49
> 7 opls_140 22 PRO HB1 2 0.06 1.008 ; qtot 0.55
> 8 opls_140 22 PRO HB2 2 0.06 1.008 ; qtot 0.61
> 9 opls_136 22 PRO CG 3 -0.12 12.011 ; qtot 0.49
> 10 opls_140 22 PRO HG1 3 0.06 1.008 ; qtot 0.55
> 11 opls_140 22 PRO HG2 3 0.06 1.008 ; qtot 0.61
> 12 opls_296 22 PRO CD 4 0.17 12.011 ; qtot 0.78
> 13 opls_140 22 PRO HD1 4 0.06 1.008 ; qtot 0.84
> 14 opls_140 22 PRO HD2 4 0.06 1.008 ; qtot 0.9
> 15 opls_235 22 PRO C 5 0.5 12.011 ; qtot 1.4
> 16 opls_236 22 PRO O 5 -0.5 15.9994 ; qtot 0.9
> ; residue 23 HYP rtp HYP q -0.4
> 17 opls_239 23 HYP N 6 -0.14 14.0067 ; qtot 0.76
> 18 opls_246 23 HYP CA 6 0.01 12.011 ; qtot 0.77
> 19 opls_140 23 HYP HA 6 0.06 1.008 ; qtot 0.83
> 20 opls_136 23 HYP CB 7 -0.12 12.011 ; qtot 0.71
> 21 opls_140 23 HYP HB1 7 0.06 1.008 ; qtot 0.77
> 22 opls_140 23 HYP HB2 7 0.06 1.008 ; qtot 0.83
> 23 opls_136 23 HYP CG 8 -0.12 12.011 ; qtot 0.71
> 24 opls_140 23 HYP HG 8 0.06 1.008 ; qtot 0.77
> 25 opls_167 23 HYP OH 8 -0.683 15.9994 ; qtot 0.087
> 26 opls_168 23 HYP HO 8 0.435 1.008 ; qtot 0.522
> 27 opls_245 23 HYP CD 9 -0.05 12.011 ; qtot 0.472
> 28 opls_140 23 HYP HD 9 0.06 1.008 ; qtot 0.532
> 29 opls_235 23 HYP C 10 0.5 12.011 ; qtot 1.032
> 30 opls_236 23 HYP O 10 -0.5 15.9994 ; qtot 0.532
> ; residue 24 GLY rtp GLY q -0.9
> 31 opls_238 24 GLY N 11 -0.5 14.0067 ; qtot 0.032
> 32 opls_241 24 GLY H 11 0.3 1.008 ; qtot 0.332
> 33 opls_298 24 GLY CA 11 0.09 12.011 ; qtot 0.422
> 34 opls_140 24 GLY HA1 11 0.06 1.008 ; qtot 0.482
> 35 opls_140 24 GLY HA2 11 0.06 1.008 ; qtot 0.542
> 36 opls_271 24 GLY C 12 0.7 12.011 ; qtot 1.242
> 37 opls_272 24 GLY O1 12 -0.8 15.9994 ; qtot 0.442
> 38 opls_272 24 GLY O2 12 -0.8 15.9994 ; qtot -0.358
> .
> .
> .
> When I grompp, I get this error :
> ERROR 1 [file topol.top, line 258]:
> No default Angle types
>
> In topol.top line 258 contain atoms 25 23 27 that are atoms OH CG CD and I added the angle between them in [angletypes] section in ffbonded.itp file.
>
> I would be grateful if anyone could shed some light on the origin of
> this error, and on what I can do to correct it.
Bonded directives in ffbonded.itp need to specify parameters in terms of atom
types, not atom names. The bonded types for the equivalent nonbonded types are
in ffnonbonded.itp, second column.
-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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