On Mon, May 29, 2017, Ake Sandgren wrote:
> I can't see any obvious problems using checkoverlap, but on the other
> hand i'm not quite sure if i'm using it correctly.
>
> The input files are available from
>
> https://web-upload.its.umu.se/dl/f/1496089012_27796/inf-nan-problem.tar.bz2
Thanks. Here's how I went about debugging the problem:
1. Always try a short run (say a one-step minimization) setting ntpr=1.
That way you get the most information. With your files, that gives this
as the mdinfo file:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 1.7616E+03 O 11561
BOND = 289.3063 ANGLE = 1322.4636 DIHED = 4107.7576
VDWAALS = NaN EEL = NaN HBOND = 0.0000
1-4 VDW = 1490.2773 1-4 EEL = 21931.0867 RESTRAINT = 0.0000
The fact that the vdw and electrostatic interactions are NaN, but other things
seem OK, is a pretty good sign that two atoms (or more) are on top of each
other.
Then, I used cpptraj
cpptraj HumanTTR_TCP_Complex_Solvated.prmtop
trajin HumanTTR_TCP_Complex_Solvated.inpcrd
checkoverlap reportfile bad-contacts.txt
go
Here is the bad-contacts.txt file:
1 Warning: Atoms 7730:WAT_688.O and 8558:WAT_964.O are close (0.00)
1 Warning: Atoms 7731:WAT_688.H1 and 8559:WAT_964.H1 are close (0.00)
1 Warning: Atoms 7732:WAT_688.H2 and 8560:WAT_964.H2 are close (0.00)
Clearly, waters 688 and 964 are in identical postions. I hope this
information will help your user track down the origin of the problem.
....dac
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Received on Wed May 31 2017 - 19:30:03 PDT
