Hi,
Yes normally I set the head and the tail on individual residues. I'm trying to make a carbohydrate residue that's not present in the preset GLYCAM parameters, a heptose specifically, by hand, and then link it to make a polysaccharide. A week ago I was able to set heads and tails of various GLYCAM residues without a problem. Now all of a sudden I can't as it gives me the error below. Why? I don't know, I haven't changed a thing in terms of settings or new programs.
Making a beta-glucose was just a simple example, in the past I would have been able to take this glucose, set it to have a head/tail of another oxygen and link another residue to it. Now I want to know why I cannot.
Here's an example of what I get.
> x = sequence { ROH 0GB }
> desc x
UNIT name: ROH
Head atom: .R<ROH 1>.A<HO1 1>
Tail atom: .R<0GB 2>.A<C2 19>
Contents:
R<ROH 1>
R<0GB 2>
> set x head x.2.O2
The value must be of the type: Atom
>
----- Original Message -----
From: "Bill Ross" <ross.cgl.ucsf.EDU>
To: amber.ambermd.org
Sent: Tuesday, May 25, 2010 1:45:03 PM GMT -05:00 US/Canada Eastern
Subject: Re: [AMBER] Setting Atom Types
> I know I've posted again but got no help. I thought I would
> try again. In any version of the leap program I'm unable to
> set the atom types on a unit. For example, I'm using the
> GLYCAM06 parameter sets. If I was to make a sequence like
> "x = sequence { ROH 0GB }", I cannot change the head and
> tail atoms via "set x head x.2.O2" or "set x tail x.2.O2"
> for example. Any ideas?
You are trying to set head on the 2nd residue, where the head
would already be joined to the tail of the first? Why? Head and
tail are normally set up on individual residues not bonded to
others.
It always helps to give your command *and* the response verbatim.
Sometimes the responses are useful for figuring out what went
wrong.
Doing a 'desc x' might help figure things out.
Bill
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Alex Boncheff
MSc. Candidate
Department of Chemistry
University of Guelph
Guelph, ON, Canada
N1G 2W1
Office: MacNaughton 233
T: 519-824-4120 x 58111
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Received on Tue May 25 2010 - 11:30:05 PDT
