Quoting David van der Spoel <[email protected]>:
On 3/3/10 8:14 PM, [email protected] wrote:
Hello,
I am trying to simulate Ethanol in water using OPLSAA. I already
tried it with all atoms, but now I want to try it with United
atoms for ethanol, i.e. CH3,CH2,OH, and HO in my topology file. I
created the topology but I got an error saying 'No bond types', so
I checked ffoplsaabon.itp file, and as the error indicated I could
not find any bond types. Is there a way for me to determine the
bonds? This is my topology file for ethanol:
[ moleculetype ]
; Name nrexcl
Ethanol 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_068 1 EOH CB 1 0 15.035
; qtot 0
2 opls_081 1 EOH CA 2 0.265 14.027
; qtot 0.265
3 opls_078 1 EOH OH 2 -0.7 15.9994
; qtot -0.435
4 opls_079 1 EOH HO 2 0.435 1.008
; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
2 3 1
3 4 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
1 2 3 1
2 3 4 1
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
1 2 3 4 3
I checked one of the paper that has been published using the same
parameters as follows:
Table 1. Potential Parameters and Molecular
Geometries of OPLS-UA and SPC/E
qa
atom or group ?, Å , kJ/mol
OPLS
R1 3.905 0.7322 0.000
R2 3.905 0.4937 0.265
-0.700
O 3.070 0.7113
H 0.000 0.0000 0.435
I would really appreciate some suggestions, on how I should tackle
the error.
Thanks
Nisha P
The united atom parameters are really leftovers from long past.
Jorgensen published his first all-atom alcohol simulations in 1988
IIRC. There is a methanol paper from 1983. Just search literature for
Jorgensen, methanol ethanol and it will show up. Then you will to type
in the parameters yourself, see chapter 5.
--
David.
Thanks David. These are the parameters I added. Do you think they seem
reasonable?
[ bondtypes ]
; i j func b0 kb
C3 C2 1 0.15300 259400.0
C2 OH 1 0.14300 267800.0
[ angletypes ]
; i j k func th0 cth
C3 C2 OH 1 108.00 100.000 ;
C2 OH HO 1 108.50 110.000
[ dihedraltypes ]
; i j k l func coefficients
C3 C2 OH HO 3 0.00000 3.49000 0.00000 3.13000 0.00000 0.00000
And this is the topology file I created using the parameters and
pdb2gmx command:
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Ethanol 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_068 1 EOH CB 1 0 15.035 ; qtot 0
2 opls_081 1 EOH CA 2 0.265 14.027
; qtot 0.265
3 opls_078 1 EOH OH 2 -0.7 15.9994
; qtot -0.435
4 opls_079 1 EOH HO 2 0.435 1.008 ; qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
2 3 1
3 4 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 4 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
1 2 3 1
2 3 4 1
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
1 2 3 4 3
Thanks
-Nisha
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[email protected] [email protected] http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536
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