Hi Gagandeep,
This way I only see the heteroatoms in colors, I want to distinguish
the positive and negative potential surfaces with colors ... not my
atoms
Myriam
gagandeep singh <gagan.sk.1994.gmail.com> escribió:
> 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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>>
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Received on Mon Oct 26 2020 - 02:30:02 PDT
