2017-02-21 12:01 GMT-07:00 Rom <[email protected]>:
> Hi guys!!
>
> I'm getting the same error as on this post (about defining the --ia-name and
> matching this to your table.xml file).
>
> My potential (table1_extrap.pot) is attached, this is the angle file I want
> to convert into gromacs format.
>
>
> My table.xml is the following, where table_end is 180 (since the angles are
> now in degrees).
>
> <cg>
> <inverse>
> <gromacs>
> <pot_max>1e8</pot_max>
> <table_end>180</table_end>
> <table_bins>0.002</table_bins>
> </gromacs>
> </inverse>
> </cg>
>
> The solution listed was to match the --ia-name to the name in the table.xml,
> but I am a bit confused, since that is not even defined in my table.xml?
> (since it was never needed when converting bonds). Am I missing something
> really obvious, what edit do I need to make?
You need a <bonded> block with the interaction name and its step size
(see attached xml file) and run:
$ csg_call --ia-name angle --ia-type angle --options table.xml
convert_potential gromacs table1_extrap.pot table_a1.xvg
(adding "--ia-name angle")
The manual is a bit unclear about that, but this will hopefully
explain it a bit better:
<https://github.com/votca/csg-manual/commit/ce1b80b12d308d2137332e98d2d457889c499c46>
Cheers,
Christoph
>
> My original run command was:
> csg_call --ia-type angle --options table.xml convert_potential gromacs
> table1_extrap.pot table_a1.xvg
>
>
> Cheers for any (what is probably very obvious lol) help!
> Rom
>
>
>
>
>
>
>
>
> On Tuesday, 14 July 2015 12:54:23 UTC+1, Albert Solernou wrote:
>>
>> Hi,
>> I think that there is a bug in csg_call, version 1.3-dev hgid:
>> 2399d10e948e. The following command:
>> csg_call --ia-type non-bonded --ia-type C6 --options table.xml
>> convert_potential gromacs B4-B4__extrapolate.pot table.xvg
>> fails with:
>> csg_get_interaction_property: bondname is undefined (when calling from
>> csg_call set it by --ia-name option)
>> It fails not matter what the value for "--ia-type" is.
>>
>> However, the same command works for version 1.2.4 hgid: 53b14819554c. I
>> can send the input B4-B4__extrapolate.pot and table.xml files, though they
>> are pretty standard.
>>
>> Best,
>> Albert
>>
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--
Christoph Junghans
Web: http://www.compphys.de
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<cg>
<bonded>
<name>angle</name>
<step>0.02</step>
</bonded>
<inverse>
<gromacs>
<pot_max>1e8</pot_max>
<table_end>180</table_end>
<table_bins>0.002</table_bins>
</gromacs>
</inverse>
</cg>
