Dear amber users,
I am using amber9 and trying to generate topology files of
4-hydroxyl-proline (PR4) under the guidance of tutorial (
http://ambermd.org/antechamber/pro4.html).
From step1 to step3, everything looks fine.
However, in step4, the command *respgen -i pro4a.mol2 -o pro4-step1.respin
-f resp1 *is supposed to generate a respin file as follows:
Resp charges for organic molecule
&cntrl
nmol = 2,
ihfree = 1,
ioutopt = 1,
&end
1.0
Resp fit for 4-OH-PRO
0 27
1 0
6 0
1 0
1 0
6 0
8 0
7 0
6 0
1 0
1 0
6 0
1 0
8 0
6 0
1 0
1 0
6 0
1 0
6 0
8 0
7 0
1 0
6 0
1 0
1 0
1 0
1 0
1.0
Resp fit for 4-OH-PRO
0 27
1 0
6 0
1 0
1 0
6 0
8 0
7 0
6 0
1 0
1 0
6 0
1 0
8 0
6 0
1 0
1 0
6 0
1 0
6 0
8 0
7 0
1 0
6 0
1 0
1 0
1 0
1 0
2
1 1 2 1
2
1 2 2 2
2
1 3 2 3
2
1 4 2 4
2
1 5 2 5
2
1 6 2 6
2
1 7 2 7
2
1 8 2 8
2
1 9 2 9
2
1 10 2 10
2
1 11 2 11
2
1 12 2 12
2
1 13 2 13
2
1 14 2 14
2
1 15 2 15
2
1 16 2 16
2
1 17 2 17
2
1 18 2 18
2
1 19 2 19
2
1 20 2 20
2
1 21 2 21
2
1 22 2 22
2
1 23 2 23
2
1 24 2 24
2
1 25 2 25
2
1 26 2 26
2
1 27 2 27
Unfortunately, the respin file I generated using the same command
looks as follows:
Resp charges for organic molecule
&cntrl
nmol = 1,
ihfree = 1,
ioutopt = 1,
&end
1.0
Resp charges for organic molecule
0 0
My mol2 files and Gaussian output files were downloaded from the
tutorial website, and I did exactly what the tutorial required.
Could someone please help me on that?
Thanks in advance!
--
Jia Xu
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Received on Wed Sep 02 2009 - 23:06:19 PDT
