The bug fix numbers 10 and 11 for amber14 talks about fixes that allows
users to use center-of-mass distance restraints in pmemd.cuda. I am
testing this functionality on a system, but cannot make it work (I get
"PMEMD Terminated Abnormally!" error message). Basically, the rst file is
as follows:
----------------- rst ------------------------
# XXXX
&rst iat = -1, -1,
iresid = 0, ir6=0,
r1 = 0, r2 = 10, r3 = 10, r4 = 100,
rk2 = 50.0, rk3 = 50.0, ialtd=0,
igr1 = 264,286,302,312,331,350,364,371,378,389,399,406,425,432,439,456,475,482,
igr2 = 6087,6090,6091,
/
&end
---------------------------------------------
The last lines of the output file is
.
.
.
LISTOUT = POUT
DISANG = rst_10
Restraints will be read from file: rst_10
Here are comments from the DISANG input file:
# XXXX
Error: Atom 1 in following group definition is greater than total #
atoms
6087
I am not sure what this error message means. Is it possible to use COM
distance restraints in pmemd.cuda yet? Thanks.
Best,
Ilyas Yildirim, Ph.D.
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Received on Tue Apr 07 2015 - 10:30:03 PDT
