[gmx-users] Reg. g_density

[Tsjerk Wassenaar]

Hi Jagan,

I just checked and indeed g_density requires a .tpr file. It would be
possible to get an approximate density using a pdb file or so, but
that requires hacking the code. For the volume it's the same thing.
The radii could be read from the file vdwradii.dat in the GMX library
directory but are better determined from the .tpr file. Also for g_sas
a .tpr file is required as it provides a more robust answer.

Cheers,

Tsjerk

On Sat, Jun 6, 2009 at 11:47 AM, Jagan Mohan<o.jagan at gmail.com> wrote:
> hello Tsjerk,
> thanks for the reply... the syntax of g_density is such that we need to
> provide a tpr file right... is there a way of doing it without the tpr...
> and also from where are the radii of the atoms read for calculation of the
> volume... or is the volume calculated differently...
> thanks in advance
>
> Regards,
> Jagan
>
> On Sat, Jun 6, 2009 at 3:10 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>>
>> Hi Jagan,
>>
>> If you provide a .tpr file, the masses will be read from there.
>> Otherwise, when providing a .gro/.pdb file or so, masses will be read
>> from the file atommass.dat in the GMX library directory.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Sat, Jun 6, 2009 at 11:25 AM, Jagan Mohan<o.jagan at gmail.com> wrote:
>> > Hey everyone,
>> > I would like to know from where does the g_density read the masses and
>> > radii
>> > of atoms to calculate the density... We do provide a tpr file but from
>> > where
>> > does it refer to and add these masses... I have a system for which i
>> > have a
>> > topology... i use this for the generation of tpr but will the masses be
>> > considered from this topology... Please do help me out...
>> >
>> > Thanks in advance
>> >
>> > Regards,
>> > Jagan
>> >
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>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
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>
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> -{[O]}-
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623