cuong nguyen wrote:
Dear Sir/Madam,
I have tried to creat the gro and top file for acid hexanoic by using
the PRODRG server. However, the atom H in -COOH group could not be found
and two O atoms are the same.
[ moleculetype ]
; Name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 DRG OAB 1 -0.767 15.9994
2 C 1 DRG CAI 1 0.343 12.0110
3 OM 1 DRG OAC 1 -0.766 15.9994
4 CH2 1 DRG CAH 1 0.048 14.0270
5 CH2 1 DRG CAG 1 0.047 14.0270
6 CH2 1 DRG CAF 1 0.047 14.0270
7 CH2 1 DRG CAE 1 0.048 14.0270
8 CH2 1 DRG CAD 2 0.000 14.0270
9 CH3 1 DRG CAA 3 0.000 15.0350
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.125 13400000.0 0.125 13400000.0 ; CAI OAB
2 3 2 0.125 13400000.0 0.125 13400000.0 ; CAI OAC
2 4 2 0.153 7150000.0 0.153 7150000.0 ; CAI CAH
4 5 2 0.153 7150000.0 0.153 7150000.0 ; CAH CAG
5 6 2 0.153 7150000.0 0.153 7150000.0 ; CAG CAF
6 7 2 0.153 7150000.0 0.153 7150000.0 ; CAF CAE
7 8 2 0.153 7150000.0 0.153 7150000.0 ; CAE CAD
8 9 2 0.153 7150000.0 0.153 7150000.0 ; CAD CAA
[ pairs ]
; ai aj fu c0, c1, ...
1 5 1 ; OAB CAG
2 6 1 ; CAI CAF
3 5 1 ; OAC CAG
4 7 1 ; CAH CAE
5 8 1 ; CAG CAD
6 9 1 ; CAF CAA
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 126.0 770.0 126.0 770.0 ; OAB CAI
OAC
1 2 4 2 117.0 635.0 117.0 635.0 ; OAB CAI
CAH
3 2 4 2 117.0 635.0 117.0 635.0 ; OAC CAI
CAH
2 4 5 2 109.5 520.0 109.5 520.0 ; CAI CAH
CAG
4 5 6 2 109.5 520.0 109.5 520.0 ; CAH CAG
CAF
5 6 7 2 109.5 520.0 109.5 520.0 ; CAG CAF
CAE
6 7 8 2 109.5 520.0 109.5 520.0 ; CAF CAE
CAD
7 8 9 2 109.5 520.0 109.5 520.0 ; CAE CAD
CAA
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 3 4 2 0.0 167.4 0.0 167.4 ; imp CAI
OAB OAC CAH
5 4 2 1 1 0.0 1.0 6 0.0 1.0 6 ; dih CAG
CAH CAI OAB
6 5 4 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF
CAG CAH CAI
7 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih CAE
CAF CAG CAH
8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD
CAE CAF CAG
9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih CAA
CAD CAE CAF
Please help me to correct this mistake.
This mailing list is for Gromacs-specific questions. For PRODRG-related issues,
please start with their FAQ (your question is answered there):
http://davapc1.bioch.dundee.ac.uk/prodrg/prodrg_faq.html
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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