Thank you Anselm,
I'm looking for afaik chimera but I can't find anything, is it a
separate extension of the program?
thanks in advance,
Myriam
"Dr. Anselm Horn" <anselm.horn.fau.de> escribió:
> 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 Mon Oct 26 2020 - 02:30:02 PDT
