Hi,
I am doing a simulation combining amber and Gaff force field (for dopc lipids),
this is the first part of my topology file:
; UNK_GMX.top created by acpypi on Thu Jun 4 22:06:03 2009
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91
0.0860
CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91
0.1094
C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91
0.0860
HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00
0.0000
O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66
0.2100
OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72
0.2104
c3 c3 12.0100 -0.12654 A 3.399676e-01
4.577296e-01 ; 1.91 0.1094
hc hc 1.0080 0.02245 A 2.649538e-01
6.568880e-02 ; 1.49 0.0157
c2 c2 12.0100 -0.15458 A 3.399676e-01
3.598240e-01 ; 1.91 0.0860
ha ha 1.0080 0.11146 A 2.599647e-01
6.276000e-02 ; 1.46 0.0150
c c 12.0100 0.44800 A 3.399676e-01
3.598240e-01 ; 1.91 0.0860
o o 16.0000 -0.47180 A 2.959927e-01
8.786400e-01 ; 1.66 0.2100
os os 16.0000 -0.15429 A 3.000018e-01
7.112800e-01 ; 1.68 0.1700
h1 h1 1.0080 0.16551 A 2.471358e-01
6.568880e-02 ; 1.39 0.0157
p5 p5 30.9700 1.14364 A 3.741781e-01
8.368000e-01 ; 2.10 0.2000
n4 n4 14.0100 0.01626 A 3.250004e-01
7.112800e-01 ; 1.82 0.1700
hx hx 1.0080 0.08244 A 1.959981e-01
6.568880e-02 ; 1.10 0.0157
OW OW 0.00000 0.00000 A 3.16572e-01 6.49775e-01 ;
1.78 0.1553
HW HW 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ;
0.00 0.0000
Na Na 0.00000 0.00000 A 2.15954e-01 1.47545e+00 ; 1.21
0.3526
Cl Cl 0.00000 0.00000 A 4.83045e-01 5.34924e-02 ; 2.71
0.0128
When I try to minimize the system, with grompp -f minimizado.mdp -c
final_system.gro -p final_system.top -o minimizado.tpr I find 2 warnings:
WARNING 1 [file final_system.top, line 19]:
Overriding atomtype c
WARNING 2 [file final_system.top, line 20]:
Overriding atomtype o
It is like it is not distinguing the capitals for amber and non-capitals for
gaff. Does anybody know which can be the cause of these warnings?
Thank you very much,
Rebeca Garcia
University of Oxford
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