Hi. I am trying to make a bond between two atoms using xleap as part
of a parameterization process for a new aminoacid residue. I have both
my protein and new residue in the same pdb file. I am using ambertools
1.5. Every time I hit the bond command, It gives out an error message.
Here are some details on my atom numbering.
The first atom is Atom number 1519. It ts a carbonyl carbon (C) in
residue 104. This should be linked to atom number 59082 wihin residue
3178 (N1). I've called the molecule in leap "mic".
I've tried:
bond 1519 59082 s
bond mic.1519 mic.59082 (and also with an "s" at the end)
bond mic.104.1519 mic.3178.59082 (same above)
bond 104.1519 3178.59082
And a few other I don't quite remember now.
Sometimes I get
bond: Argument #1 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
An other times I get some other stuff similar to that but sayng that
String is of type Double.
Anyway.
I've checked in the mailing list and other people had similar
problems, but none of the command lines I tried so far have worked.
Some help here would really be great.
Thank you
Fabrício
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Received on Wed Sep 14 2011 - 13:00:04 PDT
