RE: AMBER: antechamber

From: Ross Walker <>
Date: Wed, 7 Jun 2006 09:56:01 -0700

Dear Steve,
Here is your error:

  Max Degree = 180 NPAR= 387

So try changing this, doing a make clean and then rebuilding. Note, you may
also want to consider splitting your system into smaller fragments if that
is possible. You will probably get a better charge fit this way. This is
especially true if you have buried atoms where grid based approaches don't
tend to do well.
All the best

|\oss Walker

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From: [] On Behalf Of
Steve Seibold
Sent: Wednesday, June 07, 2006 09:17
Subject: AMBER: antechamber

I am attempting to generate lipid parameters using Antechamber. leaprc.gaff
does appear to contain all force field parameters and so no apparent
problems here. However, when I tried to calculate atomic charges, I started
running into problems. When using :


Antechamber -i LIP2.pdb -fi pdb -o LIP2 -fo perpi -nc 0 -c bcc


I get an error message in my divcon.out saying "Program terminated due to
errors" I have attached the file (divcon.out) along with my pdb file.
However, it still assigned charges in my perpi output file. I believe the
perpi charges (i.e. ANTECHAMBER_PREP.AC) are library values from AMBER
correct? I also got assigned charges AM1BCC.



I also attempted to use "resp". So, I used Gaussian to generate an output
file (pop=mk) and then used "espgen" to extract ESP information. However
when I ran:


Antechamber -I LIP2.ESP -fi gout -o LIP2 -fo perpi -nc -c resp



It appears to run, but I am suspicious. I let it run for 70 minutes and
still no print out ...nothing. So I killed it.


Does anyone know what I am doing wrong?


Thanks, Steve





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Received on Sun Jun 11 2006 - 06:07:08 PDT
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