AMBER Archive (2003)

Subject: Re: AMBER: Insight pdb file in xleap

From: Gaurav Sahni (gaurav_at_nii.res.in)
Date: Fri Aug 08 2003 - 01:25:42 CDT

Hi,
i've worked with such problems either one of two ways:
1) I have tried using the "generate.inp" script of "CNS" to remove
the INSIGHT idiosyncrasies. i believe carbohydrates can also be
generated, i.e. CNS will build you a clean PDB files (with
hydrogens). Then you could use this pdb for xleap, will be far better.
2) manually edit pdb. try, remove all hydrogens & do xleap (it'll add
the H) check errors -> edit again. this is a hit & trial process,
untill you stop getting errors, but also depends on one's comfort
with manually editing the PDB coordinate file.

hope it helps,
Gaurav Sahni 

--
you wrote:

Hello Amber users,

I loaded pdb file made by Insight in Leap (Amber7.0) and use 
"bondByDistance" command to put in bonds using default criteria.
However, some bonds are disconnected and structure is broken.
Is pdb file made by Insight different from pdb format which can be 
loaded in 
leap?

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