Hi,
Try adding the 'and' (&) operator to the mask expressions in your
second 'distance' command, e.g.
::A&:;210&@NZ,HZ1,HZ2,HZ3
which means "chain ID A and original residue number 210 and atoms NZ,
HZ1, HZ2, HZ3".
Hope this helps,
-Dan
On Tue, Mar 21, 2023 at 12:06 PM Saikat Pal via AMBER <amber.ambermd.org> wrote:
>
> Dear all,
> I want to calculate the distance between two specific residues with different chains. Here is my input:
>
> distance 179-355-dist :179.NZ,HZ1,HZ2,HZ3 :355.OE1,OE2,CD out rgs01-salt-210-lys-97-glu.dat
> distance K210A-E97D ::A:;210.NZ,HZ1,HZ2,HZ3 ::D:;97.OE1,OE2,CD out rgs01-salt-210-lys-97-glu-1.dat
> ACTION SETUP FOR PARM 'rgs01_renumber_only.pdb' (2 actions): 0: [distance 179-355-dist :179.NZ,HZ1,HZ2,HZ3 :355.OE1,OE2,CD out rgs01-salt-210-lys-97-glu.dat] :179.NZ,HZ1,HZ2,HZ3 (4 atoms) to :355.OE1,OE2,CD (3 atoms), imaged. 1: [distance K210A-E97D ::A:;210.NZ,HZ1,HZ2,HZ3 ::D:;97.OE1,OE2,CD out rgs01-salt-210-lys-97-glu-1.dat] ::A:;210.NZ,HZ1,HZ2,HZ3 (5086 atoms) to ::D:;97.OE1,OE2,CD (2130 atoms), imaged.
>
> The results are different (quite obvious because the number of atoms is different). What will be the correct syntax?
>
>
> Thanks and Regards,
> Saikat Pal
>
>
>
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Received on Tue Mar 21 2023 - 19:00:02 PDT
