Date: Fri, 23 Oct 2020 16:10:55 +0200
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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/vnd.palm attachment: ambpdb-prueba.pdb
(image/jpeg attachment: prueba.jpg)
