AMBER Archive (2004)

Subject: AMBER: (no subject)

From: HL Eastwood (s0237717_at_sms.ed.ac.uk)
Date: Fri Jul 30 2004 - 10:47:18 CDT

Hi

In essence I need to create a .crd file and a .parm file from a pdb file (which
was obtained from the Brookhaven database).

My problem is that:

1. When I load my pdb file into xleap it keeps adding countless atoms to the
system. I have tried using the "protonate" program to correct for mismatches
between the pdb system and the xleap system, but it keeps crashing out with the
following message:

UNRECOVERABLE LIBRARY ERROR:

a WRITE operation tried to write a record that was too long.

Encountered during a s sequential formatted WRITE to unit 6.

2. When I try to create a parm file using saveAmberParm <unit> something.parm
something.crd, it lists all manner of fatal errors.

My questions:

1. Is there a short and simple way of creating a parm and crd file from a pdb
file? i.e. not necessarily using xleap?
2. What is the principal difference in format between AMBER pdb files and
Brookhaven PDB files.

any help would be much appreciated

Hayden Eastwood
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