OK, I'm writing a "free-form" reader. No chain ids ever for such a file?
On Mon, Jun 25, 2012 at 11:11 AM, Robert Hanson <[email protected]> wrote:
> shame shame.
>
>
> On Mon, Jun 25, 2012 at 11:03 AM, Daniel Aioanei <[email protected]>wrote:
>
>> Thanks for looking into this issue. The pqr file I sent you was
>> created using Gromacs like this:
>>
>> g_editconf -f drgfin_GMX.tpr -mead drgfin_GMX.pqr
>>
>> On 25 June 2012 18:48, Robert Hanson <[email protected]> wrote:
>> > whatever software is creating that "PQR" file is not putting the
>> information
>> > in the correct columns:
>> >
>> > 0 1 2 3 4 5 6
>> > 7
>> >
>> 01234567890123456789012345678901234567890123456789012345678901234567890123456789
>> > xxxxxxxxyyyyyyyyzzzzzzzz
>> > ATOM 84 CA VAL A 28 2.806 7.385 9.363 1.00 99.99
>> > C
>> > ATOM 1 OAB DRG 1 -13.46000 9.99000 -8.27000 -0.7840
>> > 1.5332
>> >
>> >
>> > Jmol uses this:
>> >
>> > setAtomCoord(atom, parseFloat(line, 30, 38), parseFloat(line, 38, 46),
>> > parseFloat(line, 46, 54));
>> >
>> >
>> > So, for example, the first atom's coordinates are being read as
>> > (-13.46,0,9000)
>> >
>> > Take a look at the PDB specs. PQR is supposed to follow those.
>> >
>> >
>> >
>> > On Sun, Jun 24, 2012 at 11:10 PM, Daniel Aioanei <[email protected]>
>> wrote:
>> >>
>> >> Thanks for the sasurface/vdw explanation.
>> >>
>> >> I'm attaching the pdb and pqr files for a water molecule.
>> >>
>> >> On 25 June 2012 06:48, Robert Hanson <[email protected]> wrote:
>> >> >
>> >> >
>> >> > On Sun, Jun 24, 2012 at 8:40 PM, Daniel Aioanei <[email protected]>
>> >> > wrote:
>> >> >>
>> >> >> Dear Richard,
>> >> >
>> >> > [Bob]
>> >> >>
>> >> >>
>> >> >> Let me see if I got it right. What I need is "set solventProbe 1.4;
>> >> >> isosurface sasurface", which is also equivalent to "isosurface
>> >> >> sasurface 1.4". But while that works for larger molecules, it
>> doesn't
>> >> >> work for the water molecule.
>> >> >>
>> >> > I think I said that wrong. For water you need
>> >> >
>> >> > isosurface vdw +1.4
>> >> >
>> >> > that's different from
>> >> >
>> >> > isosurface vdw 1.4 # 1.4 ang each
>> >> >
>> >> >
>> >> >>
>> >> >> You mentioned in a previous reply that "That's a bug when the number
>> >> >> of vertices is 0. That's fixed, but for now just don't do that." I
>> >> >> just updated jmol to the latest svn version (rev. 17329) and for
>> water
>> >> >> "sasurface 1.4; show isosurface" doesn't freeze the GUI any longer,
>> >> >> but the surface is still not there. Are there any plans to make
>> >> >> sasurface work for very small molecules in the near future?
>> >> >>
>> >> >
>> >> > no. It is very important that sasurface not work for solvent. Use VDW
>> >> > +1.4
>> >> >
>> >> >>
>> >> >> As for PQR, I'm using the GAFF force field, and I'm not getting any
>> >> >> zero radii so far. But how can I load the pqr file? I tried "load
>> >> >> 'pqr::drgfin_GMX.pqr'", but the molecule just disappears when I do
>> >> >> that.
>> >> >>
>> >> >
>> >> > ?? send me the file, please.
>> >> >
>> >> >
>> >> >>
>> >> >> Thanks,
>> >> >> Daniel
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> ------------------------------------------------------------------------------
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>> >> >> _______________________________________________
>> >> >> Jmol-users mailing list
>> >> >> [email protected]
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>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Robert M. Hanson
>> >> > Larson-Anderson Professor of Chemistry
>> >> > Chair, Chemistry Department
>> >> > St. Olaf College
>> >> > Northfield, MN
>> >> > http://www.stolaf.edu/people/hansonr
>> >> >
>> >> >
>> >> > If nature does not answer first what we want,
>> >> > it is better to take what answer we get.
>> >> >
>> >> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>> >> >
>> >> >
>> >> >
>> >> >
>> >> >
>> ------------------------------------------------------------------------------
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>> >> > Exclusive live event will cover all the ways today's security and
>> >> > threat landscape has changed and how IT managers can respond.
>> >> > Discussions
>> >> > will include endpoint security, mobile security and the latest in
>> >> > malware
>> >> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> >> > _______________________________________________
>> >> > Jmol-users mailing list
>> >> > [email protected]
>> >> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>> >> >
>> >>
>> >>
>> >>
>> ------------------------------------------------------------------------------
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>> >> Exclusive live event will cover all the ways today's security and
>> >> threat landscape has changed and how IT managers can respond.
>> Discussions
>> >> will include endpoint security, mobile security and the latest in
>> malware
>> >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> >> _______________________________________________
>> >> Jmol-users mailing list
>> >> [email protected]
>> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
>> >>
>> >
>> >
>> >
>> > --
>> > Robert M. Hanson
>> > Larson-Anderson Professor of Chemistry
>> > Chair, Chemistry Department
>> > St. Olaf College
>> > Northfield, MN
>> > http://www.stolaf.edu/people/hansonr
>> >
>> >
>> > If nature does not answer first what we want,
>> > it is better to take what answer we get.
>> >
>> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Live Security Virtual Conference
>> > Exclusive live event will cover all the ways today's security and
>> > threat landscape has changed and how IT managers can respond.
>> Discussions
>> > will include endpoint security, mobile security and the latest in
>> malware
>> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> > _______________________________________________
>> > Jmol-users mailing list
>> > [email protected]
>> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>> >
>>
>>
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond. Discussions
>> will include endpoint security, mobile security and the latest in malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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