> 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.C1.C2
> :1.C3.C4.C5.C6.C7.C8.C9.C10.C11.C12.C13.C14.C15.C16.C17.C18.C19.C20.C21.C2
> 2.N1.N2.N3.N4.N5.N6.N7.N8.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.C3.C4.C5.C6.C7.C8.C9.C10.C11.C12.C13.C14.C15.C16.C17.C18.C19.C20.C21.C2,:2-57
Or, if you are using everything except for :1.C1,C2, try
^:1.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.
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Received on Wed Aug 10 2005 - 23:53:01 PDT
