RE: AMBER: creating pdb file....

From: Ross Walker <>
Date: Tue, 14 Jun 2005 10:51:21 -0700

Dear Vijay,

> First I used mdcrd file and I tried to generate pdb
> file to see my structure with ambpdb command but it
> state error as below:

Ambpdb will only work with restart or inpcrd files. It does not work with
trajectory files. If you want to extract specific frames (or all frames)
from an mdcrd file as pdb's then use ptraj. However, it is very rare that
you would want to do this since handling a single mdcrd file (for use in VMD
or analysing in ptraj) is much easier than several thousand pdb files.

> After i getting this kind of message I tried use rst
> file to generate pdb file. But i get the same thing as
> below:
> [vijay.glycomm03 test1]$ ambpdb -p <
> micelwat_md1_rst.traj > micelrst.pdb

I suspect that this is an unpatched version of ambpdb. The ambpdb that
shipped with Amber 8 was a static memory version and so would crash with
large systems. Apply bugfix.29 (see, make
clean, recompile and then try it.

Alternatively if all you want to do is visualise the structure the latest
version of VMD (v1.8.3) can now read both trajectory (mdcrd - select crd or
crdbox) and restart (select rst7) files. See for

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Jun 14 2005 - 18:53:00 PDT
Custom Search