From: <davide.savy.unina.it>
Date: Tue, 16 Oct 2012 15:28:27 +0200

Hello everyone!
I am trying to create prmtop and inpcrd files with 22 sodium
benzoates, 22 sodium ions and 200 waters. To do that, I created a
benzoate (without sodium ions) with xLeap, then I saved it as a pdb
file. I used this pdb file to run packmol and obtain 22 benzoate
(still without sodium ions) packed with 200 waters. Since I need
charges for my benzoates, I cannot use directly this pdb file into
Leap, thatís why I also created a mol2 file containing only benzoate
(without sodium ions) with xLeap. Then, I ran this mol2 file into
antechamber and parmcheck. Contemporarily, I extracted all the info
about the solute (benzoates) from the output file coming from packmol
and I converted this extracted pdb file into a mol2 file using babel.
After that, I took the info about atom types, subst_id, charges root
atoms (in the TRIPOS SUBSTRUCTURE) from the mol2 file coming from
antechamber and I put them in the mol2 file coming from babel. Also, I
took all the info about the from the mol2 file coming from antechamber
into the mol2 file coming from babel. After that, I run tLeap, using
the mol2 file created as explained before and a pdb file containing
only the info about the 200 waters, created with packmol.
This method seems to work, but it is quite tricky and is subjecetd to
Please, find attached a file with the path I follow to get the prmtop
and inpcrd files.

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Received on Tue Oct 16 2012 - 06:30:03 PDT
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