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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Received on Fri Oct 23 2020 - 08:30:02 PDT
