Re: [AMBER] positional and NMR distance restraints together

From: David A Case <>
Date: Tue, 2 Mar 2021 09:13:25 -0500

On Tue, Mar 02, 2021, Qinghua Liao wrote:

>    RESTRAINT  =      705.1138 (positional restraints)

I think this is wrong: the 705 number is the sum of all restraints, both
positional and NMR.
>While the other one failed to distinguish positional and NMR distance
>    RESTRAINT  =     1175.6790
>    NMR restraints: Bond = 1175.679   Angle =     0.000   Torsion =   0.000

This looks like there are no postional restraints, (or the coordinates are
identical to those in the -ref file). You should double-check the mdout
file to make sure that you actually have positional restraints turned on
(ntr=1) here.

>I tried pmemd.cuda (single version), it worked....

Are you saying the the identical job gave different results depending on
which version of pmemd you used? Have you run jobs with just 5 steps of
minimization, settting ntpr=1, and compared the outputs in detail? Compare
the results of this short run to those from a CPU run.

Finally, do you have large forces in your system? pmemd.cuda can fail at
the minimization stage when the are bad contacts.


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Received on Tue Mar 02 2021 - 06:30:02 PST
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