AMBER Archive (2004)

Subject: RE: AMBER: (no subject)

From: HL Eastwood (s0237717_at_sms.ed.ac.uk)
Date: Fri Jul 30 2004 - 13:12:34 CDT

Hi Ross

Attached are the pdb files that I used. The large one (1E4R.pdb) is a sample of
20 NMR structures for MBD-8 (Mouse beta defensin). The small file (nmr.1.pdb)
is a single NMR structure that was extracted from the larger file. nmr.1.pdb is
the structure I;ve attempted to use.

You said: "How much have you "massaged" the pdb file?"

On the smaller structure I have replaced CYS by CYX and I've removed the
connectivity information. However, this hasn;t changed the error message I
getwhen I employ the "protonate" script.

You said: "What do you need your prmtop file for? Do you want it just for
visualisation purposes or to run a simulation?"

In answer, I want to:

1. employ the "carnal" package to calculate a set of average trajectories for
the 20 NMR structures (that I;ll then store in a file of pdb format)

2. Perform a minimization and MD simulation on one of the structures.

Many thanks

Hayden


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