[AMBER] Parametrisation of ligand with ions

From: julian.zachmann selvita.home.pl <julian.zachmann.selvita.home.pl>
Date: Fri, 13 May 2016 11:30:27 +0200 (CEST)

Dear Amber-Users,

I am automating a protocol to parametrise ligands with ions. As an example I use
ATP with two magnesium ions. I am aware that I could load ATP in tleap and
randomly add magnesium ions but this is not what I want.

I have calculated ESP of this system with Jaguar and now I try to create the
prepi and frcmod files and I have tried various ways:

1. "antechamber -i mol.out -fi jout -o mol.prepi -fo prepi -c resp" is not
working for me because it needs Gaussian output. In the manual it says
antechamber could read Jaguar output but here it tells me:

"Sorry, RESP charge needs a Gaussian output file (gout) with -gv = 0 or a gesp
file with -gv = 1"

2. I found this post in the archives from 2008 so I don't know how up-to-date it

"Jaguar can write out the esp file to be used by resp. You may first read in a
jaguar output and write out an ac or mol2 file. Then use respgen to generate the
resp input files (two stages). Then run two-stage resp to generate resp charges
(input files from respgen, esp file from jaguar). Finally, you read in resp
charges to the ac or mol2 file with antechamber (for example: antechamber -fi ac
-fo ac -i mol.ac -o mol.ac -c rc -cf QOUT). That's it."

I did not find the option to write out an "esp-file" with jaguar but can write
out an ac or mol2 file which contains the correct ESP charges.

espgen says to only use Gaussian output (in the manual) and the shell it tells

espgen -i jaguar.out -o mol.esp

Error: No ESP fitting centers and fitting values exist, adding 'iop(6/33=2)
iop(6/42=6)' to the key word list

I found that respgen has the option "-f resp4 - calculating ESP from point
charges" so I tried:

respgen -i mol.ac -o mol.esp -f resp4

but this didn't seem to work because after (like in the manual):

respgen -i mol.ac -o mol.respin1 -f resp1
respgen -i mol.ac -o mol.respin2 -f resp2
resp -O -i mol.respin1 -o mol.respout1 -e mol.esp
resp -O -i mol.respin1 -o mol.respout1 -e mol.esp -t qout_stage1
resp -O -i mol.respin2 -o mol.respout2 -e mol.esp -t qout_stage2 -q qout_stage1

I get this mistake:

At line 840 of file resp.F (unit = 10, file = 'mol.esp')
Fortran runtime error: Bad value during integer read

3. antechamber -fi ac -i mol.ac -fo prepi -o mol.prepi

parmchk2 -i mol.prepi -f prepi -o mol.frcmod

First complains this:

For atom[8]:O8, the best APS is not zero, bonds involved by this atom are frozen

For atom[44]:Mg44, the best APS is not zero, bonds involved by this atom are

For atom[45]:Mg45, the best APS is not zero, bonds involved by this atom are

And then:

Atom type of Mg does not shown up in PARMCHK.DAT

If I indicate parmchk2 to look in a different parameter file, I lose all the
other atoms.


I don't know what else to do. Could anybody please advise me on this?

Best wishes,

AMBER mailing list
Received on Fri May 13 2016 - 03:00:04 PDT
Custom Search