Hello i am very new to molecular mechanics so please excuse me if my questions
are a little naive or stupid.I am trying to minimise a mol2 file with
topolbuild1_3 using the following command line arguments from within the
topolbuild directory:
./topolbuild -dir /usr/local/gromacs/share/gromacs/top -ff oplsaa
-n /Users/bioinformatics/Desktop/zinc_12404782 -purge 0 -move
I get the following error: Fatal error.Source code file: topolbuild.c, line:
345Cannot open log file zinc_12404782.log
I realise that i will have to go over the parameters again but i was hoping for
some sort of output. Does anyone know if it is a problem with the parameters of
the input file shown below or some problem with the way in which topolbuild is
called ? I am a little unsure how to point to the oplsaa force fields?
Thanks Andrew
mol2 file:
@<TRIPOS>MOLECULEZINC12404782 36 38 0 0
0SMALLUSER_CHARGES[(3R)-1-(1-naphthyl)pyrrolidin-3-yl]methanamine@<TRIPOS>ATOM
1 C1 4.9121 5.4361 -0.0609 C.ar 1 <0> -0.1104
2 C2 3.7311 6.1754 -0.0451 C.ar 1 <0> -0.1149 3
C3 2.5180 5.5573 -0.0225 C.ar 1 <0> -0.1069 4 C4
2.4527 4.1553 -0.0151 C.ar 1 <0> -0.0508 5 C5
3.6528 3.4026 -0.0311 C.ar 1 <0> -0.0373 6 C6
4.8869 4.0753 -0.0543 C.ar 1 <0> -0.1044 7 C7
3.5890 1.9989 -0.0232 C.ar 1 <0> -0.1128 8 C8
2.3798 1.3731 -0.0007 C.ar 1 <0> -0.0985 9 C9
1.1942
2.1013 0.0157 C.ar 1 <0> -0.1624 10 C10 1.2135
3.4800 0.0087 C.ar 1 <0> 0.0930 11 N1 0.0208
4.1998 0.0243 N.pl3 1 <0> -0.4642 12 C11 -1.1513
3.2890 -0.0264 C.3 1 <0> 0.0276 13 C12 -2.3059
4.1663 0.5194 C.3 1 <0> -0.1388 14 C13 -1.6180
4.9899 1.6322 C.3 1 <0> -0.1313 15 H1 -1.7859
4.5266 2.6045 H 1 <0> 0.1043 16 C14 -0.1188
4.9670 1.2811 C.3 1 <0> 0.0431 17 C15 -2.1414
6.4276 1.6324 C.3 1 <0> 0.0042 18 H2 5.8616
5.9505 -0.0790 H 1 <0> 0.1273 19 H3 3.7785
7.2544
-0.0504 H 1 <0> 0.1244 20 H4 1.6108 6.1430
-0.0060 H 1 <0> 0.1264 21 H5 5.8102 3.5153
-0.0664 H 1 <0> 0.1319 22 H6 4.4986 1.4167
-0.0357 H 1 <0> 0.1310 23 H7 2.3403 0.2939
0.0049 H 1 <0> 0.1276 24 H8 0.2481 1.5807
0.0339 H 1 <0> 0.1299 25 H9 -1.3545 2.9801
-1.0518 H 1 <0> 0.1004 26 H10 -0.9921 2.4211
0.6135 H 1 <0> 0.0709 27 H11 -3.0996 3.5449
0.9341 H 1 <0> 0.0885 28 H12 -2.6948 4.8209
-0.2606 H 1 <0> 0.0875 29 H13 0.4419 4.4789
2.0783
H 1 <0> 0.0705 30 H14 0.2477 5.9836 1.1382 H
1 <0> 0.0961 31 H15 -1.5362 7.0345 2.3058 H
1 <0> 0.1357 32 H16 -2.0827 6.8358 0.6235 H
1 <0> 0.1409 33 H17 -3.9079 7.3788 2.0939 H
1 <0> 0.4420 34 H18 -4.1089 5.8327 1.5151 H 1
<0> 0.4364 35 N2 -3.5360 6.4306 2.1084 N.4 1
<0> -0.6468 36 H19 -3.5649 6.0740 3.0708 H 1
<0> 0.4397@<TRIPOS>BOND 1 1 6 ar 2 1 2 ar 3
1 18 1 4 2 3 ar 5 2 19 1 6 3 4 ar 7 3
20 1 8 4 10 ar 9 4 5 ar 10 5
6 ar 11 5 7 ar 12 6 21 1 13 7 8 ar 14 7
22 1 15 8 9 ar 16 8 23 1 17 9 10 ar 18 9 24
1 19 10 11 1 20 11 16 1 21 11 12 1 22 12 13 1 23
12 25 1 24 12 26 1 25 13 14 1 26 13 27 1 27 13
28 1 28 14 15 1 29 14 16 1 30 14 17 1 31 16 29 1
32 16 30 1 33 17 31 1 34 17 32 1 35 17 35 1 36 33
35 1 37 34 35 1 38 35 36 1@<TRIPOS>
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