Sorry I see now that there are instruction in the 18-amber manual on setting the path for skf files,
I will try this and you can disregard my question.
Kind regards,
Pär
________________________________
From: Pär Håkansson <par.hakansson.oulu.fi>
Sent: 31 May 2019 14:08
To: amber.ambermd.org
Subject: [AMBER] Boron QM/MM
Dear amber-suport,
I would like to perform QM/MM with a molecule contain Boron atom.
If I specify QM method as qm_theory ='SCC-DFTB', I get, since this is a non-standard atom,
the error message:
Parameter files:
TYP (AT) TYP (AT) SK integral FILE
| 1 1 (B ) 1 (B ) /appl/chem/amber/18/dat/slko/mio-1-1/B-B.skf
****************************************************
* !! A FILE NEEDED BY DFTB WAS NOT FOUND !! *
****************************************************
Missing file:
/appl/chem/amber/18/dat/slko/mio-1-1/B-B.skf
I then downloaded a set of Bron skf files to from
http://www.dftb.org, that I gave to
the administrator of the supercomputer I am using.
However, it would be best not to put these in the same mio-1-1/ directory since they are
generated with a different procedure and are now in /appl/chem/amber/18/dat/slko/matsci-0-3/.
My problem is that sander.MPI still search in mio-1-1 and I get
Missing file:
/appl/chem/amber/18/dat/slko/mio-1-1/B-B.skf.
Is there a way to make sander search in matsci-0-3/ ? Or do people make a soft link (ln -s) ?
Any advise is very welcome.
Kind regards,
Pär
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 31 2019 - 06:00:04 PDT
