Why not try the latest AmberTools package, which is free ...
Ray
On Fri, Apr 19, 2013 at 2:43 PM, Wang Bo <dadiaobo.gmail.com> wrote:
> Hello,
>
> I am currently using AMBER9 to do MMPBSA calculation for a series of
> compounds that contains one or more halogen atoms.
> I know this is an old version but it is the only version on the
> supercomputer I am using right now and I have to wait to few month to
> update the computer and software.
>
> The error messages I got are:
> "No radius found for Br1 4083 in residue <0> 276"
> "Died at /N/soft/linux-sles9-ppc64/
> amber9-ibm-64/src/mm_pbsa/mm_pbsa_calceneent.pm line 502, <PDB> line 4085."
> I searched the archive and the solution I found is to add the radius
> information manually to mm_pbsa_calceneent.pm.
> Here is what I added:
> "F" => 1.470 + 1.400,
> "Cl" => 1.750 + 1.400,
> "Br" => 1.850 + 1.400,
> "I" => 1.980 + 1.400,
>
> But this did not work, I got the same error message again.
> Then I read the mm_pbsa_calceneent.pm again, what I found is in the sub of
> make_pqr_file(), how this script to find the atom type is using the whole
> atom name first and then the first character of the atom. If the atom did
> not in the list, then the radius was not found.
> Here is a problem for halogen atoms, if the atom name is "F" "Cl" "Br", it
> can works well, however, if I have multiple halogen atoms, named "Cl1"
> "Br2", then I think Cl1 will be treated as C - carbon, and Br2 was not
> found.
>
> Can anyone tell me how do I treat the multi halogen atoms situation? For
> example, if I changed all atom names of chlorine to "Cl", what will happen?
> Is it OK that not each atom has a unique atom name? Or is there any way to
> solve this problem rather than use the latest version?
>
>
> --
> Sincerely,
> Bo Wang
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Received on Fri Apr 19 2013 - 15:00:03 PDT
