Re: [AMBER] xleap problem for terminal DNA base pairs.

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sun, 20 Jun 2010 10:18:37 -0700

> However, I found all the terminal residues's PO2 atoms cannot be
> recongized by the program. I double checked the name of the atoms
> in my pdb file. For example the first base pairs is named as DA,
> where the PO2 atom name are as follows P and O1P and O2P.
> They should be recongizable in xleap. Similarly, I found the
> residue A in the middle of the DNA are using the same names, and
> able to be recongized by xleap.

Leap maps terminal residues to e.g. DA5 and DA3 via a residue
name map defined in the leaprc. You can get around this by using
your own leaprc without that setting, or by using loadpdbusingsequence
or some such command - 'help' in leap will list it.

However you may be better served by the default terminal residue
types, and in this case you would delete the extra phosphates from
your pdb.

If you want phosphates at both ends, you may need to create your own
phosphate residue template - not sure if one exists.


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Received on Sun Jun 20 2010 - 10:30:03 PDT
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