AMBER Archive (2009)

Subject: [AMBER] minimization error

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Fri Oct 02 2009 - 06:42:54 CDT

dear Amber !

I have build a model for DNA junction.
I have a problem in running the minimization in vaccum, when I load the molecule in leap it have not
showed any error .
1. I loaded the molecule and when i saved the parameter file it gave the following warning

--------------------------------------------------------------

Building improper torsion parameters.
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-C-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ** Warning: No sp2 improper torsion term for NB-CA-CB-CB
        atoms are: N7 C6 C5 C4
 ** Warning: No sp2 improper torsion term for N*-CB-CB-NC
        atoms are: N9 C5 C4 N3
 ------------------------------------------------------

but the .inpcrd and .prmtop files got saved

2) when i do the minimization in vaccum it
sander got stoped and it gave the following error

----------------------------------------------------------
At line 1262 of file _ew_box.f
Fortran runtime error: Bad value during integer read
----------------------------------------------------------

what is the problem with the molecule and what one should do to
correct it

thanks in advance

balaji
UOM

                                               
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