Dear Prof. Case;
{{ Sorry I did not notice, while replying it was sent personally to your mail id. }}
Thanks, the patch you suggested (indicated with + signs) I have applied and its working fine now as default angles being 90 90 90.
>> Can you say when "earlier" was that things worked?
>> I can't find which older code might have worked here
I was using AmberTools1.2 earlier (installed with bug fixes, 5-6 months
back) and was getting all the angles. But recently these strange things
happened, but I am not able to recall the 'exact' things (pardon me):
1) Recently due to reasons, I removed the AMBER and again installed AT1.2, with all bug fixes last week only and was not able to get the angles
2) This might be funny, but I was not
able to reproduce it again. When I was not getting angles using set UNIT box {. . .}, I checked solvatebox command working fine or not. YES it
was working fine, then in same xleap terminal I again used set UNIT box
command, to my surprise I was getting angles!. It seemed to me as Xleap
is learning the things. Though it never worked again.
thanks,
________________________________
From: David A Case <case.biomaps.rutgers.edu>
To: Jio M <jiomm.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, June 29, 2012 9:32 PM
Subject: Re: [AMBER] Fw: set box problem
On Fri, Jun 29, 2012, Jio M wrote:
>
> command is: set w1 box {188 191 166}
>
>
> earlier I used to get box angles 90 90 90 in inprcrd and prmtop but
> I am not getting it now as shown below.
I can't find which older code might have worked here, but the current code
is not setting the box angle when "set <unit> box" is executed. If you create
a new unit, then the default box angle is 90, but this doesn't get done if
you use the "set" command to modify an existing unit.
Here is a proposed patch:
--- AmberTools/src/leap/src/leap/unit.c
+++ AmberTools/src/leap/src/leap/unit.c
.. -1450,6 +1450,7 .. ASSOC aAssoc;
case ODOUBLEid:
dX = dODouble(oAttr);
UnitSetBox( uUnit, dX, dX, dX );
+
UnitSetBeta( uUnit, 90.0*DEGTORAD );
UnitSetUseBox( uUnit, TRUE );
break;
case LISTid:
.. -1471,6 +1472,7 .. ASSOC aAssoc;
if ( i==3 ) {
UnitSetBox( uUnit, daVector[0], daVector[1], daVector[2] );
UnitSetUseBox( uUnit, TRUE );
+ UnitSetBeta( uUnit, 90.0*DEGTORAD );
}
break;
case NULLid:
....dac
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Received on Fri Jun 29 2012 - 20:30:02 PDT
