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 - 15:00:02 PDT
