Be careful here. Atom types are case sensitive. The gaff force
field is all lower case, while parm99 is upper case. I think
antechamber is only formally for gaff, so you'll have to switch
case at the least to use parm99.
HTH - John
On Wed, 13 Aug 2003, Yong-Liang Zhu wrote:
> Thank Rhonda for responding. However, when I altered the prepin file, for
> exmple
>
> A line generated by antechamber:
> 19 C1 ca M 17 ....
>
> I altered to
> 19 C1 cb M 17 ....
>
>
> Then parmchk had problem to recognize cb. It even ask to revise the mass of
> cb in the frcmod file generated, like
> cb 0.000 0.000 ATTN, need revision
>
> So why cb, cc, n*, nc are in parm99.dat and do not work here?
>
> Thank you.
>
> Yong
> -----Original Message-----
> From: Rhonda Torres [mailto:torres.scripps.edu]
> Sent: Wednesday, August 13, 2003 3:38 PM
> To: amber.scripps.edu
> Subject: Re: AMBER: Atom type in prepin file
>
>
> Hi Yong,
>
> Antechamber only uses the chemical symbol (C, O, H, etc.) that
> corresponds to the atom number of your purine-like compound.
> You will likely have to appropritately alter the Antechamber generated
> file prior to import into leap (prepin).
>
> Rhonda
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Received on Thu Aug 14 2003 - 01:53:00 PDT
