I used "verbosity 2" while trying to work out precisely what was going on.
:-) Lachele
Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: Thursday, March 01, 2012 1:19 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] EP Question
On Thu, Mar 01, 2012, B. Lachele Foley wrote:
>
> 1. People include angle and torsion parameters for EP's in their parm files.
>
> 2. Leap completely ignores them. (I read the code... really... it's coded this way.)
These two are correct, I think.
>
> 3. As a bonus, despite EP's being included in the "Atom Types" list,
> leap complains "(UNKNOWN ATOM TYPE: EP)".
This should not happen; and it does sound like a problem with the addAtomTypes
command (probably in a leaprc file.) I tried this:
tleap -f leaprc.ff12SB
loadAmberParams frcmod.tip4pew
saveAmberParm TP4 prmtop incprd
didn't see any UNKNOWN ATOM TYPE messages. Also tried this:
tleap -f leaprc.leaprc.GLYCAM_06EP
saveAmberParm 4GB prmtop inpcrd
again, no UNKNOWN ATOM TYPE message. So, exactly what are you doing to get
such messages?
....dac
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Received on Thu Mar 01 2012 - 11:00:02 PST
