Hi Justin
Cheers. I have attached my pentane itp file. The cage itp is formatted
the same. In the examples there never seems to be [atom types] included.
I have included it. Does it seem O.K?
Gavin
Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Mark.
>>
>> I have looked this up, but I am a little uncertain. Does one of the
>> topologies have to be included within the other as an .itp file. If so
>
> No. You #include .itp files to simply add molecules within a .top; it
> would be very rare to #include an .itp within an .itp (although it can
> be done). For your case, your .top is simple:
>
> #include (force field)
>
> #include "cage.itp"
> #include "pentane.itp"
>
> [ system ]
> My system
>
> [ molecules ]
> Cage 1
> Pentane 1
>
>> do I only define the [defaults directive] in the .top file i.e. I take
>> it I don't include this directive in the .itp file as well.
>>
>
> The [defaults] directive is provided by whatever force field you
> #include. If you're using some custom parameters, then it needs to be
> defined once (and only once) at the top of your .top file. Otherwise,
> you'll get fatal errors from grompp.
>
> -Justin
>
>> Cheers
>>
>> Gavin
>>
>> Mark Abraham wrote:
>>> Look up the include file mechanism on the webpage.
>>>
>>> Mark
>>>
>>> ----- Original Message -----
>>> From: Gavin Melaugh <gmelaug...@qub.ac.uk>
>>> Date: Tuesday, September 28, 2010 19:04
>>> Subject: [gmx-users] topology file for two molecules
>>> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>>>
>>>> Hi all
>>>>
>>>> I want to run a simulation of one tert-pentane molecule inside one
>>>> organic cage molecule. I have the topology files for both
>>>> molecules but
>>>> obviously I only need one .top file as the input for grompp.
>>>> What is the
>>>> most convenient way of having both topologies in one file?
>>>>
>>>> Many Thanks
>>>>
>>>> Gavin
>>>> --
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>>
>
[atomtypes]
;type mass charge ptype sigma(nm) epsilon(kjmol-1)
CT 12.011000 -0.180000 A 0.350000 0.276144
HC 1.008000 0.060000 A 0.250000 0.125520
;Molecular level
[moleculetype]
; name nrexcl
tertpentane 3
[atoms]
; atomnr type resnr residue name cgnr charge mass
1 CT 1 PENT CT 1 0.0000 12.0110
2 CT 1 PENT CT 1 -0.1800 12.0110
3 CT 1 PENT CT 1 -0.1800 12.0110
4 CT 1 PENT CT 1 -0.1800 12.0110
5 CT 1 PENT CT 1 -0.1800 12.0110
6 HC 1 PENT HC 1 0.0600 1.0080
7 HC 1 PENT HC 1 0.0600 1.0080
8 HC 1 PENT HC 1 0.0600 1.0080
9 HC 1 PENT HC 1 0.0600 1.0080
10 HC 1 PENT HC 1 0.0600 1.0080
11 HC 1 PENT HC 1 0.0600 1.0080
12 HC 1 PENT HC 1 0.0600 1.0080
13 HC 1 PENT HC 1 0.0600 1.0080
14 HC 1 PENT HC 1 0.0600 1.0080
15 HC 1 PENT HC 1 0.0600 1.0080
16 HC 1 PENT HC 1 0.0600 1.0080
17 HC 1 PENT HC 1 0.0600 1.0080
[bonds]
; ai aj func b0(nm) kb(kjmol-1 nm-2)
1 2 1 0.1529 224262.4
1 3 1 0.1529 224262.4
1 4 1 0.1529 224262.4
1 5 1 0.1529 224262.4
2 6 1 0.1090 284512.0
2 7 1 0.1090 284512.0
2 8 1 0.1090 284512.0
3 9 1 0.1090 284512.0
3 10 1 0.1090 284512.0
3 11 1 0.1090 284512.0
4 12 1 0.1090 284512.0
4 13 1 0.1090 284512.0
4 14 1 0.1090 284512.0
5 15 1 0.1090 284512.0
5 16 1 0.1090 284512.0
5 17 1 0.1090 284512.0
[angles]
; ai aj ak func theta(deg) ktheta(kjmol-1 rad-2)
2 1 3 1 112.70 488.2728
2 1 4 1 112.70 488.2728
2 1 5 1 112.70 488.2728
3 1 4 1 112.70 488.2728
3 1 5 1 112.70 488.2728
4 1 5 1 112.70 488.2728
1 2 6 1 110.70 313.8000
1 2 7 1 110.70 313.8000
1 2 8 1 110.70 313.8000
6 2 7 1 107.80 276.1440
6 2 8 1 107.80 276.1440
7 2 8 1 107.80 276.1440
1 3 9 1 110.70 313.8000
1 3 10 1 110.70 313.8000
1 3 11 1 110.70 313.8000
9 3 10 1 107.80 276.1440
9 3 11 1 107.80 276.1440
10 3 11 1 107.80 276.1440
1 4 12 1 110.70 313.8000
1 4 13 1 110.70 313.8000
1 4 14 1 110.70 313.8000
12 4 13 1 107.80 276.1440
12 4 14 1 107.80 276.1440
13 4 14 1 107.80 276.1440
1 5 15 1 110.70 313.8000
1 5 16 1 110.70 313.8000
1 5 17 1 110.70 313.8000
15 5 16 1 107.80 276.1440
15 5 17 1 107.80 276.1440
16 5 17 1 107.80 276.1440
[dihedrals]
; ai aj ak al func V1 V2 V3
V4 (all kj mol-1)
3 1 2 6 5 0.00000 0.00000 1.25520
0.00000
3 1 2 7 5 0.00000 0.00000 1.25520
0.00000
3 1 2 8 5 0.00000 0.00000 1.25520
0.00000
4 1 2 6 5 0.00000 0.00000 1.25520
0.00000
4 1 2 7 5 0.00000 0.00000 1.25520
0.00000
4 1 2 8 5 0.00000 0.00000 1.25520
0.00000
5 1 2 6 5 0.00000 0.00000 1.25520
0.00000
5 1 2 7 5 0.00000 0.00000 1.25520
0.00000
5 1 2 8 5 0.00000 0.00000 1.25520
0.00000
2 1 3 9 5 0.00000 0.00000 1.25520
0.00000
2 1 3 10 5 0.00000 0.00000 1.25520
0.00000
2 1 3 11 5 0.00000 0.00000 1.25520
0.00000
4 1 3 9 5 0.00000 0.00000 1.25520
0.00000
4 1 3 10 5 0.00000 0.00000 1.25520
0.00000
4 1 3 11 5 0.00000 0.00000 1.25520
0.00000
5 1 3 9 5 0.00000 0.00000 1.25520
0.00000
5 1 3 10 5 0.00000 0.00000 1.25520
0.00000
5 1 3 11 5 0.00000 0.00000 1.25520
0.00000
2 1 4 12 5 0.00000 0.00000 1.25520
0.00000
2 1 4 13 5 0.00000 0.00000 1.25520
0.00000
2 1 4 14 5 0.00000 0.00000 1.25520
0.00000
3 1 4 12 5 0.00000 0.00000 1.25520
0.00000
3 1 4 13 5 0.00000 0.00000 1.25520
0.00000
3 1 4 14 5 0.00000 0.00000 1.25520
0.00000
5 1 4 12 5 0.00000 0.00000 1.25520
0.00000
5 1 4 13 5 0.00000 0.00000 1.25520
0.00000
5 1 4 14 5 0.00000 0.00000 1.25520
0.00000
2 1 5 15 5 0.00000 0.00000 1.25520
0.00000
2 1 5 16 5 0.00000 0.00000 1.25520
0.00000
2 1 5 17 5 0.00000 0.00000 1.25520
0.00000
3 1 5 15 5 0.00000 0.00000 1.25520
0.00000
3 1 5 16 5 0.00000 0.00000 1.25520
0.00000
3 1 5 17 5 0.00000 0.00000 1.25520
0.00000
4 1 5 15 5 0.00000 0.00000 1.25520
0.00000
4 1 5 16 5 0.00000 0.00000 1.25520
0.00000
4 1 5 17 5 0.00000 0.00000 1.25520
0.00000
--
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