Hi,
On Tue, Sep 27, 2011 at 2:16 PM, Bala subramanian
<bala.biophysics.gmail.com> wrote:
> acceptor resname atomname atomnameH | mask mask maskH | clear | print
The 'acceptor mask' form of the acceptor command requires two masks
(mask and maskH), one for the heavy atom and one for the corresponding
hydrogen atom. Try this instead:
acceptor mask :149-183.NH1 :149-183.1HH1
acceptor mask :149-183.NH1 :149-183.2HH1
Also, if you want to make sure that only atoms from ARG residues are
selected, append '&:ARG' to your masks, e.g.:
donor mask :149-183.OD1&:ARG
donor mask :149-183.OE1&:ARG
acceptor mask :149-183.NH1&:ARG :149-183.1HH1&:ARG
acceptor mask :149-183.NH1&:ARG :149-183.2HH1&:ARG
-Dan
>
> I just want to select ARG in the resid range 149-183 and the corresponding
> hydrogens bonded to NH1 atom of ARG.
>
>
> 1)
>
> donor mask :149-183.OD1
> donor mask :149-183.OE1
> acceptor mask :149-183.1HH1
> acceptor mask :149-183.2HH1
>
> 2)
> donor mask :149-183.OD1
> donor mask :149-183.OE1
> acceptor mask :149-183.NH1,1HH1
> acceptor mask :149-183.NH1,2HH1
>
> PTRAJ: rms reference out X4U_V3.rms :149-183.CA,C,N
> Mask [:149-183.CA,C,N] represents 105 atoms
>
> PTRAJ: donor mask :149-183.OD1
> Mask [:149-183.OD1] represents 3 atoms
>
> PTRAJ: donor mask :149-183.OE1
> Mask [:149-183.OE1] represents 1 atoms
>
> PTRAJ: acceptor mask :149-183.NH1,1HH1
> WARNING in ptraj, acceptor: Error in mask specification. Ignoring...
>
> PTRAJ: acceptor mask :149-183.NH1,2HH1
> WARNING in ptraj, acceptor: Error in mask specification. Ignoring...
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Received on Tue Sep 27 2011 - 12:00:03 PDT
