The steps were completed. But when typing the following command:
saveamberparm complex 1FKO_sus.prmtop 1FKO_sus.inpcrd The following error
appears:
FATAL: Atom .R<GLN 242>.A<OE1 8> does not have a type. FATAL: Atom .R<GLN
242>.A<NE2 9> does not have a type. FATAL: Atom .R<PRO 243>.A<N 1> does not
have a type. FATAL: Atom .R<PRO 243>.A<CA 2> does not have a type. FATAL:
Atom .R<PRO 243>.A<C 3> does not have a type. FATAL: Atom .R<PRO 243>.A<O
4> does not have a type. FATAL: Atom .R<PRO 243>.A<CB 5> does not have a
type. FATAL: Atom .R<PRO 243>.A<CG 6> does not have a type. FATAL: Atom
.R<PRO 243>.A<CD 7> does not have a type. Failed to generate parameters
Parameter file was not saved. >
2018-04-16 14:30 GMT-03:00 David A Case <david.case.rutgers.edu>:
> On Mon, Apr 16, 2018, Edjan Silva wrote:
>
> > Okay. Tutorial gives an example using protein with ff99SB force field. I
> > want to make molecular dynamics using DNA, so use parm99 force field?
>
> By no means! Please read the force fields chapter in the Reference
> Manual for an explanation of various options, and our recommendations
> for which force fields to use.
>
> Tutorials (which can and do get out of date) should be viewed as aids in
> learning how to use Amber. They should not be viewed as "cookbook"
> examples to be copied verbatim. One indication of this is that ff99SB
> is now in the "oldff" (old force field) directory, indicating that it
> should only be used to check or extend some old simulations.
>
> ...regards...dac
>
>
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Received on Mon Apr 16 2018 - 12:00:02 PDT
