Dear amber developers and users,
Recently I tried to repeat the Advanced Tutorial 16 titled "An Amber Lipid
Force Field Tutorial"
I tried to repeat the example concerning Rhodopsin.
So I downloaded the step5_assembly.pdb file, I converted it using
charmmlipid2amber.x script and as the examples says, I tried to load the pdb
file to tleap using leaprc.lipid11 and leaprc.ff99SB force field files.
However I get errors for the protein part.
In the example it is written "This formatted PDB file can now be processed
via the script charmmlipid2amber.x. Once the file has been processed, the
next step is to start LEaP. In LEaP, a force field for the protein can be
loaded along with the Lipid11 force field. Then it is possible to load the
structure and build the parameter and topology file in LEaP.
By searching the amber mailing list I found one reply from Ross
http://archive.ambermd.org/201205/0170.html concerning the errors i got,
saying that "You will need to remove these from the file, run the script to
convert the lipid naming and then manually put the water and protein back
in. These are pretty advanced calculations so you will need to do a lot of
the leg work yourself I'm afraid. It will be quite a while until everything
can be properly automated I'm afraid. "
If this is the case, I would suggest to correct the tutorial, mentioning
what Ross decribed, because it took me several days searching in amber
mailing list to understand what was the error.
Thanks for your time
Dr George Lamprinidis
*---------------------------------------------*
|Dr George Lamprinidis |
|Researcher & Laboratory Assistant Staff |
|School of Health Sciences |
|Faculty of Pharmacy |
|National & Kapodistrian University of Athens |
|Greece |
|tel: +30 2107274304 |
| +30 2107274521 |
|fax: +30 2107274747 |
|e-mail: lamprinidis.pharm.uoa.gr |
| geolampr.gmail.com |
*---------------------------------------------*
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Received on Thu Aug 01 2013 - 06:30:03 PDT
