AMBER Archive (2009)

Subject: Re: AMBER: a question about ff03ua

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Fri Jan 02 2009 - 09:30:46 CST

        
        
        
        
        

Dear All,

For example, for n-dodecane, I tried
to generate a mol2 file by hand. I
attached the mol2 file to the mail. I arraged the charges for C-H and
C-H-H interactions and then I erased H atoms. All
the charges in the file is zero. Then I tried
to generate a prep file, but I got this message in below. Could you
help me to generate prep file from the mol2 file?

Thanks
in advance

Sincerely

[root_at_fencevrepc-84-23 dodecaneuamol2]#
antechamber -i dodecaneuamol2.mol2 -fi mol2 -o dodecaneuamol2.prep
-fo prepi -c resp -nc 0 -at amber -rn DEC

Warning: the assigned bond types may be
wrong, please :

(1) double check the structure (the
connectivity) and/or

(2) adjust atom valence penalty
parameters in APS.DAT, and/or

(3) increase MAXVASTATE in define.h and
recompile bondtype.C

(4) increase PSCUTOFF in define.h and
recompile bondtype.C

    Be cautious, use a large value of
PSCUTOFF (>10) will significantly increase the computer time

Error: cannot run
"/usr/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of
antechamber.c properly, exit

[root_at_fencevrepc-84-23 dodecaneuamol2]#

--- On Thu, 12/25/08, David A. Case <case_at_biomaps.rutgers.edu> wrote:
From: David A. Case <case_at_biomaps.rutgers.edu>
Subject: Re: AMBER: a question about ff03ua
To: amber_at_scripps.edu
Date: Thursday, December 25, 2008, 3:01 PM

On Thu, Dec 25, 2008, oguz gurbulak wrote:
>
> I
> tried to prepare a structure to get the prmtop and inpcrd input files
> for ff03ua force field. And I did all the operations in below. But
> after I got the frcmod file , I realized that there are some AA force
> field parameters in it. So I thougt that I didn't / couldn't
generate
> a UA prepin file for my MD simulations.

Antechamber inherently works in an all-atom environment. You can't use
it to generate united atom parameters.

It's not even clear what would qualify as a "ff03ua" force field
for
octane: ff03ua was parameterized for amino acids, and it is not clear
(to me) that there exists a systematic procedure for generating the UA
forcefield for arbitrary molecules.

For octane, you might try this: generate a mol2 file by hand, with the
same carbon paramters used for aliphatic side chains. All the charges
will be zero (more or less required). This should get you something
compatible with ff03ua -- no guarantees at all about comparison to
experiment! You might also see what something like opls/ua has done for
alkanes.

...good luck...dac

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