Greetings,
When I try to do a post-MD minimization with sander, I get the following
error:
At line 828 of file ew_box.F90
Fortran runtime error: Bad value during integer read
Error termination. Backtrace:
#0 0x2ad124e7ef1a
#1 0x2ad124e7fa75
#2 0x2ad124e8022c
#3 0x2ad124f49df3
#4 0x2ad124f4dfa4
#5 0x5624a57d1991
#6 0x5624a57cc3ae
#7 0x5624a57cdc16
#8 0x5624a57685e8
#9 0x5624a5732978
#10 0x5624a5731799
#11 0x5624a573188f
#12 0x2ad1256d43f0
#13 0x5624a56aeba9
#14 0xffffffffffffffff
I suspect that the problem is the format of the starting crd file, which is
the last MD frame:
Cpptraj Generated trajectory
>
> 6.002 28.808 38.770 5.349 28.929 38.009 5.818 29.557 39.422
> 5.759
> 27.897 39.133 7.355 28.814 38.116 7.492 29.807 37.688 8.469
> 28.684
> 39.190 9.417 29.048 38.793 8.265 29.292 40.072 8.677 27.281
> 39.756
> 7.958 27.079 40.550 8.433 26.501 39.036 10.081 26.948 40.276
> 10.730
Unlike the starting crd that I generated with tleap:
default_name
> 3940
> 5.9680000 28.8220000 38.7230000 5.2970000 28.8960000 37.9720000
> 5.8560000 29.5950000 39.3630000 5.8170000 27.9530000 39.2180000
> 7.3610000 28.8280000 38.1620000 7.5100000 29.8150000 37.7240000
> 8.4280000 28.6770000 39.2670000 9.3670000 29.0100000 38.8240000
Thereby, I convert the last MD frame to pdb format, I load the pdb into
tleap and save it back as a .crd file. Sander runs normally afterwards. I
am just wondering, is there any direct way to write the last MD frame to
the right crd format?
--
======================================================================
Dr Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
&
CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
Brno, Czech Republic
email: tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 30 2018 - 16:00:03 PDT
