Thanks Justin.
I already added the description in the ffbonded.itp, but nothing is shown in
the topol file. I am not sure to put atom names (e.g. C9 C10) or atom type (C
C)? However, I tried both and non of them worked. I don't know what I am doing
wrong and I appreciate if you could help me resolve my issue.
Kind regards,
Ehsan
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-us...@gromacs.org
Sent: Thursday, December 12, 2013 3:02:22 PM
Subject: Re: [gmx-users] OPLS force field parameters
On Thu, Dec 12, 2013 at 12:45 PM, Ehsan Sadeghi es...@sfu.ca 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.
[ NAF ]
[ atoms ]
C1opls_966 0.3846 1
C2opls_966 0.3846 1
C3opls_966 0.3846 1
C4opls_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
C5opls_966 0.3846 1
C6opls_966 0.3846 1
C7opls_966 0.3846 1
C8opls_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
C9opls_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
Note that assigning all atoms to a single charge group is inappropriate.
Surely grompp will warn about this, but you should construct the groups
more carefully.
snip
However, the parameters that we had in topol file are different:
[ bonds ]
; aiaj functc0c1c2c3
1 2 1
1 5 1
[ angles ]
; aiajak functc0c1c2
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?
I answered this already:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-December/086118.html
You provide the parameters in ffbonded.itp, grompp goes and finds them. If
something is missing, grompp fails.
-Justin
--
==
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==
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