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, that’s 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
mistakes.
Please, find attached a file with the path I follow to get the prmtop
and inpcrd files.
Thanks,
Davide
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Received on Tue Oct 16 2012 - 06:30:03 PDT
