Date: Fri, 23 Oct 2020 18:57:09 +0530
Hi Myrian,
Follow these simple steps in chimera. After getting the surface view of
your system, go to actions-->colour-->by heteroatoms. You will get the
image something like attached here. I hope this is what you are looking for.
Regards,
Gagandeep
On Fri, Oct 23, 2020 at 8:59 PM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
> Hi Myriam,
>
> you did not say how you wanted to compute the surface, but asked just
> for the charges ...
>
> The ambpdb command writes the charges in the occupancy row, and probably
> chimera does not use that information. But AFAIK chimera can import
> top/crd files and then thus should be able to compute a charge-mapped
> surface.
>
> Otherwise, you could try to project that occupancy entries from your pdb
> file onto the surface. VMD can do that (I bet, chimera as well).
>
> Regards
>
> Anselm
>
>
> On 10/23/2020 04:10 PM, MYRIAN TORRES RICO wrote:
> > Hi David,
> >
> > Finally, I used ambpdb -p file.top -c file.crd -pqr file.pdb and I have
> > obtained the file attached (ambpdb-prueba.pdb), but when I open this
> > file.pdb in chimera por example, and I calculate the potencial
> > electrostatic surface, the red and blue zones don't appear...(prueba.jpg
> > attached)
> >
> > Any suggest?
> >
> > Thanks so much in advance,
> >
> >
> > Myriam
> >
> >
> >
> > David A Case <david.case.rutgers.edu> escribió:
> >
> >> On Fri, Oct 23, 2020, MYRIAN TORRES RICO wrote:
> >>>
> >>> I want to calculate the potential surface of my protein, for this I
> >>> need the charges of all the amino acids in the pdb, but they don't
> >>> come ... how could I calculate them, with RESP?
> >>
> >> If you want the partial charges on each atom, look in this folder:
> >> $AMBERHOME/dat/leap/lib, and choose the force field you want. For
> >> the ff14SB and ff19SB force fields, look in amino12.lib for most
> >> residues, aminont12.lib for N-terminal residues and aminoct12.lib for
> >> C-terminal residues.
> >>
> >> You could also check out the Cornell et al paper, which shows them in a
> >> visual format. This is reference 30 in the Amber 2020 Reference Manual.
> >>
> >> ....dac
> >>
> >>
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> >
> >
> >
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(image/png attachment: image.png)
