Hello. Thank you for the reply. It really was kind of stupid to me to
leave the double-quote open. As for the / character missing, there is
no second line in my file. The email server must have formatted the
text, and the result was a second line. But anyway, thank you for the
tip.
I have corrected the input and the dist.RST file now looks like this
# Distance restraint for chain A and B (center of mass)
&rst restraint="distance (com(1-33.N,CA,C),com(34-66.N,CA,C))", r1=0.,
r2=11., r3=11., r4=35.0, rk2 = 30., rk3 = 30.,
When I type the pmemd command, a warning appears on screen stating that:
At line 990 of file nmr_calls.F90 (unit = 33, file = 'dist.RST')
Fortran runtime error: Cannot match namelist object name restraint
I have simply copied and modified a bit the lines on the amber12
manual that state:
The following are all examples of valid restraint definitions:
restraint = "distance( (45) (49) )"
= "angle (:21.C5’ :21.C4’ 108)"
= "torsion[-1,-1,-1, com(67, 68, 69)]"
= "angle( -1, plane(81, 85, 87, 90) )"
= "angle(plane(com(9,10),:5.CA,31,32),plane(14,15,15,16))"
= "coordinate(distance(:5.C3’,:6.O5’),-1.0,distance(134,-1),1.0)"
What am I doing wrong here?
Thank you
Fabrício
2012/9/18 David A Case <case.biomaps.rutgers.edu>:
> On Mon, Sep 17, 2012, Fabrício Bracht wrote:
>>
>> And the dist.RST file I have used
>>
>> &rst restraint = "distance(com(1-33.N,CA,C) com(34-66.N,CA,C)), r1=0.,
>> r2=11., r3=11., r4=35.0, rk2 = 30., rk3 = 30.,
>
> Sorry: I missed this in the earlier email. The above file won't work:
> first, the opening double-quote for restrain is never closed; second, there
> is no "/" character signifying the end of the namelist block.
>
> ...dac
>
>
> _______________________________________________
> 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 Tue Sep 18 2012 - 19:30:04 PDT
