[AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files

From: Marek Maly <marek.maly.ujep.cz>
Date: Thu, 20 Aug 2020 12:21:08 +0200


I would like to draw attention to a problem regarding the specific use of
the antechamber and parmchk / parmchk2 programs, starting with the
AmberTools17 version. It is the use of these routines to create mol2 and
frcmod outputs from the mol2 input, where the only operation required is
to add gaff atom types to the mol2 output file and eventually to create
also the appropriate frcmod file. The input mol2 file is in my case
obtained as the output from R.E.D. IV program, used for calculation of
partial charges using RESP method. At first I thought that the problem
with this relatively simple action, which the antechamber and parmchk
programs handled easily until version 16, is due to the presence of the
foreign chemical element "Si" (atom no. 80) in my residues, but as it
turned out (after the Si - substitution Si - > C in the input mol2 file)
this problem is more general in nature. Unfortunately, the problem
persists even after this substitution and even after disabling the
acdoctor routine (running antechamber with "-dr no") and possibly
"freezing" non-standard bonds in the input mol2 file with "f". In the best
(AT19) case, all key Amber files are created:


which are moreover identical (except for the letter "f" for frozen bonds)
to the same files produced by AmberTools16.

However, my calculation script in AmberTools19 case still ends with an
absurd error:

"Unable to find charges in file (Mol_m1-o1-sm.mol2)"

where Mol_m1-o1-sm.mol2 is the input mol2 file. This is of course
nonsense, considering the existence of all the Amber files mentioned
above. So in spite the perfect creation of all *.AC, *.AC0 and INF files
neither the output mol2 file nor the frcmod file is created.

I would be very grateful for advice on how to get such great output with
AmberTools19 or later (mol2 file with added atom types and possibly frcmod
file - it is clear to me that in the case of a foreign chemical element,
the frcmod file will not contain concrete bond / nonbond values
parameters) as could be obtained using antechamber and parmchk in
AmberTools16 and older versions. This functionality is key for my work and
I hope there exists a more elegant solution than maintaining an
alternative old version of AmberTools16 just for this specific need.

The inputs and outputs for one specific residue are available in the
attached file, namely:

#1 AmberTools16
a) using parmchk
b) using parmchk2
There are identical mol2 outputs but different frcmod outputs (in case b)
is this file empty)

#2 AmberTools19
a) using parmchk2 (without modifying the input mol2 script and without
adding the "-dr no" parameter to the antechamer command)

b) using parmchk2 (unusual "Si-x" bonds are frozen with "f" and the
antechamber is started with the parameter "-dr no")

You may easily try/check also the case, were the "Si" atom (number 80) is
substituted with "C" atom, and "-dr no" + "f" are eventually used.


input mol2 file: Mol_m1-o1-sm.mol2
calculation script: MakePREPandCHECK_MOL2_TO_MOL2.sh
output mol2 file: Mol_m1-o1-sm_withAT.mol2 (created just in AT16 case)
output frcmod file: Mol_m1-o1-sm.frcmod (created just in AT16 case, please
notice the difference between parmchk ans parmchk2 case).

Then there are the usual Amber outputs and StdOut and ErrOut files
(SCREEN_OUTPUT_ATxy.txt, ERR_ATxy.txt) with informations/errs reported by
antechamber/parmchk/2 programs on the screen.

Thank you very much in advance for any useful comments!

       Best wishes,


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Received on Thu Aug 20 2020 - 03:30:02 PDT
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