Sending your complete output file might also help to diagnose the
problem. How far does sander get before the segmentation fault occurs?
-Dan
On Tue, Sep 28, 2010 at 9:04 AM, subrata paul <paul.subrata34.gmail.com> wrote:
> dear sir,
> First we creat 10 disaccharide in xleap using GLYCAM_06 force field.
> then we
>>solvatebox 10_disa SPCBOX 3.0
> This is not a cubic box .
> to make cubic box we set..
>> set 10_disa box {32.0 32.0 32.0}
>> saveamberparm 10_disa xxx.prmtop xxx.inpcrd
>
> is it creat cubic box.
> then i minimize the system *min.in
> *&cntrl
> imin=1,
> maxcyc=2500,
> ncyc=1000,
> ntb=1,
> ntr=0,
> cut=12
> /
> During minimization by sander * segmentation fault* is coming out.
> where is error...? kindly help me.
>
> thanking you
> subrata
>
> On Tue, Sep 28, 2010 at 3:52 PM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Tue, Sep 28, 2010, subrata paul wrote:
>> >
>> > I am simulating 10 disaccharide and 1000 (aprx) SPC/E water molecules.
>> after
>> > solvating i made cubic box
>> > >set *mixer* box { 32.0 32.0 32.0}
>>
>> Sorry: we still need information about what you really did. What do you
>> mean
>> by "after solvating"? If you used "solvateBox", then the box information
>> is
>> already associated with the system. But we need the *full* set of commands
>> in
>> order to provide any help.
>>
>> ....dac
>>
>>
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>>
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Received on Tue Sep 28 2010 - 09:00:13 PDT
