On Wed, Apr 13, 2016 at 6:22 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
> Jason,
> Thanks for your reply.
>
> I checked the number of atoms for my system and it is as follows:
>
> Mutant_complex: 3930
> Mutant_A : 3021
> B: 909
>
> For wild type:
> Wild_complex: 3944
> A : 3035
> B: 909
>
>
> There is difference in atom numbers between prmtop from wild type Vs Mutant
> for complex and protein A but isn't the change in atom number expected as
> we are deleting extra atoms to mutate to alanine? The wildtype nA + nB =
> number of atoms in the wildtype complex. Same for mutant as well. But the
> error is saying that it is not the case.
> I also tried to manually change the atom number in mutant to match the atom
> number of the wild type but got different error message. Any thoughts on
> this would be helpful.
>
Never change the contents of the prmtop file (unless you are absolutely
certain you know what you're doing... and even then, still don't).
> Also, you mentioned about changing the flags in the command line in the
> previous email. Do you mind explaining that a little bit more? All the
> receptor and ligand protein are already specified. So I was wondering what
> else we could change/check for flags?
>
Since the numbers you showed above *are* consistent, I suspect you have a
typo in your command-line. Look for a place where you may have
accidentally swapped mutant or wild-type prmtop names. Since you've never
posted the command-line that you used, I can't help spot anything.
The error message you are hitting is a *very* simplistic check. It takes
the atom numbers from each prmtop (the same numbers I had you look for in
the prmtop file), adds them up for the receptor and ligand, and checks that
it is the same number as in the complex. If it's not, it prints the error
you're seeing. There is very little room for a bug in this particular
check (especially since it's known to work correctly in the tests and
tutorial). I strongly suspect you are making a mistake somewhere in your
command-line that will appear obvious once you see it.
HTH,
Jason
--
Jason M. Swails
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Received on Wed Apr 13 2016 - 19:30:03 PDT
