Antechamber is designed for much smaller molecules. Standard
parameters and charges for RNA exist in the Amber forcefields, and
most people would just use these. If you have a particular reason to
reparametrise RNA nucleotides using any of the methods in
antechamber, then you would be best advised to do it
residue-by-residue.
Dave
Dr David Evans
London School of Pharmacy
---- Message from Cenk Andac <cenk_andac.yahoo.com> at 2004-10-08
02:31:18 ------
>
>Hi,
>
>I would like to assign atomic charges in sybyl format using
ANTECHAMBER for a 16nt RNA hairpin. When I execute the following
antechamber command
>
>
>
>// antechamber -s 2 -i tar.pdb -fi pdb -o tar.mol2 -fo mol2 /
>
>-at sybyl -c bcc -nc -15 -j 4
>
>
>
>I keep getting this MAXATOM failure:
>
>
>
>// The atom number exceeds the MAXATOM, reallocate memory
>
>// Running: /home/jenk/amber8/exe/atomtype -i ANTECHAMBER_AC.AC0 /
>
>-o ANTECHAMBER_AC.AC -p sybyl
>
>// Cannot open file ANTECHAMBER_AC.AC, exit
>
>
>
>I have 518 atoms in my RNA molecule. Could anyone out there let me
know
>
>please how to adjust MAXATOM size?
>
>Regards,
>
>Jenk Andac
>
>Ph.D. Dissertator
>
>University of Wisconsin-Madison WI
>
>Faculty Candidate in Turkey
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Received on Fri Oct 08 2004 - 11:53:00 PDT
