just want to correct, we used "ff14SBonlysc" with GB8 in this paper.
Hai
On Mon, Dec 8, 2014 at 7:39 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Mon, Dec 08, 2014, ROOPALI VERMA wrote:
>>
>> I am trying to create my prmtop and inpcrd file from tleap of amber12 for
>> that i have created leaprc file
>>
>> source leaprc.ff96
>
> My geuss is that the error is in the "source leaprc.ff96" step: this is not a
> recommended ff, and its leaprc file is in the "oldff" directory. Hence, no
> protein libraries were loaded. You should see the following line in your
> output:
>
> Could not open file leaprc.ff96: not found
>
> [Developers: I'm thinking we should make this a fatal error, rather than just
> a warning.]
>
> You should be *sure* that this is the forcefield you really want. It has
> rather poor secondary structure preferences. I am aware of claims that
> this can be somewhat ameliorated by combining it with certain GB models, but
> am not (personally) fully convinced. You should also consider using ff14SB
> plus igb=8:
>
> %A H. Nguyen
> %A J. Maier
> %A H. Huang
> %A V. Perrone
> %A C. Simmerling
> %T Folding Simulations for Proteins with Diverse Topologies Are Accessible in
> Days with a Physics-Based Force Field and Implicit Solvent
> %J J. Am. Chem. Soc.
> %V 136
> %P 13959-13962
> %D 2014
>
> ...good luck....dac
>
>
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Received on Mon Dec 08 2014 - 20:30:02 PST
