[gmx-users] OPLS force field issue
Ehsan Sadeghi
esa38 at sfu.ca
Mon Dec 9 21:05:56 CET 2013
Thanks Justin.
I added the bond description in the ffbonded.itp but it does not show in the topol.top file.
In ffbonded.itp we have:
[ bondtypes ]
; i j func b0 kb
OW HW 1 0.09572 502080.0 ; For TIP4F Water - wlj 1/98
OW LP 1 0.01750 753120.0 ; -idem-
C* HC 1 0.10800 284512.0 ;
C1 C2 1 0.16020 292880.0 ;
C2 C3 1 0.16020 292880.0 ;
" I am not sure to put C C or C1 C2 here; I tried both, neither worked."
[ angletypes ]
; i j k func th0 cth
HW OW HW 1 109.500 627.600 ; For TIP4F Water - wj 1/98
HW OW LP 1 54.750 418.400 ; For TIP4F Water - wj 1/98
OU U OU 1 180.000 1255.200 ; J Phys Chem 97, 5685 (1993)
HC C* CW 1 126.800 292.880 ;
HC C* CB 1 126.800 292.880 ;
HC CS CW 1 126.800 292.880 ;
----------------
However, the parameters that we had in topol file are different:
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 5 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 5 1
2 1 6 1
5 1 6 1
--------------------------------
How gromacs can find c0, c1,c2 and c3 from b0, kb, th0, and cth in the ffbonded.itp?
Thanks a lot,
Ehsan
----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Friday, December 6, 2013 11:28:01 AM
Subject: Re: [gmx-users] OPLS force field issue
On 12/6/13 1:46 PM, Ehsan Sadeghi wrote:
> Hi gmx users,
>
> I try to use OPLS force field for my simulation. I added the following residue to the aminoacids.rtp, but when I generate the topol.top file it does not show the the bond stretching, angle bond, dihedrals. Where should I add these properties? It seems different from gromos where you can add g_a, g_b, and g_d in fbonded.itp.
>
OPLS atom types have opls_* names and what are called "bonded atom types" (in
the second column of ffnonbonded.itp). These atom types are used in
ffbonded.itp to define bonded interactions. When grompp is called, parameters
are read from ffbonded.itp and written into the .tpr file. If parameters are
missing for a given combination, a fatal error is triggered. Of course, one
should always be able to add the parameters directly in the .rtp, or even the
.top, if desired.
-Justin
> Thanks,
> Ehsan
>
> [ NAF ]
> [ atoms ]
> C1 opls_966 0.3846 1
> C2 opls_966 0.3846 1
> C3 opls_966 0.3846 1
> C4 opls_966 0.3846 1
> F17 opls_972 -0.1923 1
> F18 opls_972 -0.1923 1
> F19 opls_972 -0.1923 1
> F20 opls_972 -0.1923 1
> F21 opls_972 -0.1923 1
> F22 opls_972 -0.1923 1
> F23 opls_972 -0.1923 1
> F24 opls_972 -0.1923 1
> C5 opls_966 0.3846 1
> C6 opls_966 0.3846 1
> C7 opls_966 0.3846 1
> C8 opls_966 0.3846 1
> F25 opls_972 -0.1923 1
> F26 opls_972 -0.1923 1
> F27 opls_972 -0.1923 1
> F28 opls_972 -0.1923 1
> F29 opls_972 -0.1923 1
> F30 opls_972 -0.1923 1
> F31 opls_972 -0.1923 1
> F32 opls_972 -0.1923 1
> C9 opls_966 0.3846 1
> C10 opls_966 0.3846 1
> C11 opls_966 0.3846 1
> C12 opls_966 0.3846 1
> F33 opls_972 -0.1923 1
> F34 opls_972 -0.1923 1
> F35 opls_972 -0.1923 1
> F36 opls_972 -0.1923 1
> F37 opls_972 -0.1923 1
> F38 opls_972 -0.1923 1
> F39 opls_972 -0.1923 1
> F40 opls_972 -0.1923 1
> C13 opls_966 0.3846 1
> C14 opls_966 0.3846 1
> C15 opls_967 0.3218 1
> C16 opls_966 0.3846 1
> F41 opls_972 -0.1923 1
> F42 opls_972 -0.1923 1
> F43 opls_972 -0.1923 1
> F44 opls_972 -0.1923 1
> F45 opls_973 -0.1641 1
> F46 opls_972 -0.1923 1
> F47 opls_972 -0.1923 1
> C48 opls_968 0.3228 1
> O49 opls_980 -0.2742 1
> C50 opls_969 0.401 1
> O51 opls_981 -0.2604 1
> C52 opls_967 0.3218 1
> C53 opls_971 0.3216 1
> F55 opls_974 -0.1637 1
> F56 opls_974 -0.1637 1
> F57 opls_975 -0.1932 1
> C58 opls_970 0.4947 1
> F59 opls_977 -0.1662 1
> F60 opls_977 -0.1662 1
> F61 opls_978 -0.3278 1
> F62 opls_978 -0.3278 1
> F66 opls_976 -0.1649 1
> F67 opls_976 -0.1649 1
> F68 opls_976 -0.1649 1
> S54 opls_979 1.4124 1
> O63 opls_982 -0.632 1
> O64 opls_982 -0.632 1
> O65 opls_982 -0.632 1
> [ bonds ]
> C1 C2
> C2 C3
> C3 C4
> C4 C5
> C5 C6
> C6 C7
> C7 C8
> C8 C9
> C9 C10
> C10 C11
> C11 C12
> C12 C13
> C13 C14
> C14 C15
> C15 C16
> F17 C1
> F18 C1
> F19 C2
> F20 C2
> F21 C3
> F22 C3
> F23 C4
> F24 C4
> F25 C5
> F26 C5
> F27 C6
> F28 C6
> F29 C7
> F30 C7
> F31 C8
> F32 C8
> F33 C9
> F34 C9
> F35 C10
> F36 C10
> F37 C11
> F38 C11
> F39 C12
> F40 C12
> F41 C13
> F42 C13
> F43 C14
> F44 C14
> F45 C15
> F46 C16
> F47 C16
> C15 O49
> O49 C48
> F55 C48
> F56 C48
> C48 C50
> F57 C50
> C50 C58
> C58 F66
> C58 F67
> C58 F68
> C50 O51
> O51 C52
> C52 F59
> C52 F60
> C52 C53
> C53 F61
> C53 F62
> C53 S54
> S54 O63
> S54 O64
> S54 O65
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
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
==================================================
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