Re: [AMBER] Prep file is empty

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Thu, 30 Jan 2014 08:21:22 +0100

Dear Debostuti Ghosh Dastidar,

I think BF4 has a total charge of -1; so this is BF4(-)

You could use R.E.D. Server Dev. & R.E.D. python at:
   http://q4md-forcefieldtools.org/REDS-Development/
& http://q4md-forcefieldtools.org/REDS-Development/news.php
   http://q4md-forcefieldtools.org/REDS-Development/images/RED-Python.gif

The format of the FF library used is mol2/mol3 (and not prep): see:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php

You can download the R.E.D. Python job for BF4(-) I ran for you at:
http://q4md-forcefieldtools.org/Help/P10290.tar.bz2
  See
http://q4md-forcefieldtools.org/Help/P10290/

The inputs I used:
http://q4md-forcefieldtools.org/Help/P10290/Mol_red1.pdb
http://q4md-forcefieldtools.org/Help/P10290/Project.config
(all RED Python defaults are used, but the total charge which equals -1)
See http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/readme.txt

The FF lib (output):
http://q4md-forcefieldtools.org/Help/P10290/Data-R.E.D.Server/Mol_m1/Mol-sm_m1-c1.mol2

The frcmod file lists the unknown FF parameters (output); well boron
is not known...
http://q4md-forcefieldtools.org/Help/P10290/Data-R.E.D.Server/Data-Default-Proj/frcmod.unknown
can be easily resolved...
a frcmod.used file can be provided as input to solve that...
See http://q4md-forcefieldtools.org/REDS-Development/RED-Server-demo1.php
     http://q4md-forcefieldtools.org/REDS-Development/popup/poptestcase.php

The leap script (output):
http://cluster.q4md-forcefieldtools.org/~fydred/Project/P10290/Data-R.E.D.Server/Data-Default-Proj/leaprc.ff13q4mdfft

I hope this helps.

regards, Francois

Read more:
  http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/readme.txt
  http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/Project.config
  http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/Configuration.py


> I have calculated esp charges for BF4 using gaussian G09.While converting
> the log file to the prep file using antechamber, the Fluorine atoms are not
> being recognized and NEWPDB is empty. However, there was no error shown
> while running antechamber. The log file and the corresponding mol2 file are
> fine. I have tried using the -j flag but it did not help. On using -s 2 the
> following are shown
>
> Running: /usr/local/bin/amber12//bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
>
> Running: /usr/local/bin/amber12//bin/prepgen -i ANTECHAMBER_PREP.AC -f int
> -o BF4_ani.prep -rn "MOL" -rf molecule.res



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Received on Wed Jan 29 2014 - 23:30:02 PST