sure - sorry for the lack of information. So I ran the minimization
without periodic boundary condition and it work - so during the
generation of prmtop/inpcrd without adding any water to the system
also no boundary conditions were added - so my solution would be to
copy the pbe from the first prmtop/inpcrd and use that - from the
manual it looks like it is the last line in the inpcrd file so paste
it into the new inpcrd file would that solve the problem?
On Thu, Jan 19, 2012 at 1:49 PM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Thu, Jan 19, 2012, Jorgen Simonsen wrote:
>>
>> I have one protein structure where I have to change a residue and need
>> the same amount of water molecules for each simulation - so I solvate
>> one and then make a pdb file changing the residues' properties when I
>> do the minimization amber does not produce any output but just
>> "hangs". I have look into the generation of the prmtop and inpcrd
>> files and I do not get any error messages there. I get warnings on how
>> close the atoms are together. I do not know how to debug the problem
>> with the new prmtop/inpcrd. My minimization looks like this
>
> Try running with maxcyc=1: do you get any energy on the first step? Assuming
> the answer is "no", you'll probably have to post your system. Note that
> sander doesn't take pdb files as input, so it's not possible to figure out
> exactly what you did in between changing the pdb file and running sander.
> Maybe if you gave a more detailed description, someone could help.
>
> ...dac
>
>
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Received on Thu Jan 19 2012 - 05:30:03 PST
