AMBER Archive (2005)

Subject: Re: AMBER: ptraj command inputs

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Wed Aug 10 2005 - 17:43:31 CDT

> solvent here). The problem is that two atoms in residue 1 are group one,
> but all the other atoms in residue 1 as well as other residues in the
> molecule are in group 2. If I use the commands below ptraj only uses the
> parts that pertain to residue 1, ignoring residues 2 through 57. Other
...
> trajin tmp.mdcrd 1 2 1
> radial tmp 0.1 70 :1_at_C1@C2
> :1_at_C3@C4_at_C5@C6_at_C7@C8_at_C9@C10_at_C11@C12_at_C13@C14_at_C15@C16_at_C17@C18_at_C19@C20_at_C21@C2
> 2_at_N1@N2_at_N3@N4_at_N5@N6_at_N7@N8_at_N9@N10 2-57

You cannot have a space between the two designators for the "solvent" (or
any mask in general) since each will be interpreted as separate strings,
i.e. the 2-57 will be ignored. Moreover, 2-27 is not a complete
designation, you need to specify :

   :1_at_C3@C4_at_C5@C6_at_C7@C8_at_C9@C10_at_C11@C12_at_C13@C14_at_C15@C16_at_C17@C18_at_C19@C20_at_C21@C2,:2-57

Or, if you are using everything except for :1_at_C1,C2, try

^:1_at_C1@C2

There is a command in rdparm called "checkmask" that you can use to check
to see what atoms are selected for a specified mask.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu