Hi dear David.
Thanks a lot for your help. I tried to use default ions, but when i tried
to save prmtop and inpcrd file, I got a message that said:
For atom: .R<CO 405>.A<CO 1> Could not find vdW (or other) parameters for
type: Co2+
For atom: .R<Cl- 406>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<CO 407>.A<CO 1> Could not find vdW (or other) parameters for
type: Co2+
For atom: .R<Cl- 408>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<CO 409>.A<CO 1> Could not find vdW (or other) parameters for
type: Co2+
For atom: .R<Cl- 410>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<CO 411>.A<CO 1> Could not find vdW (or other) parameters for
type: Co2+
For atom: .R<Cl- 412>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<CO 413>.A<CO 1> Could not find vdW (or other) parameters for
type: Co2+
For atom: .R<Cl- 414>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<CO 415>.A<CO 1> Could not find vdW (or other) parameters for
type: Co2+
For atom: .R<Cl- 416>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 417>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 418>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 419>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 420>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 421>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 422>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 423>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 424>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
atom: .R<Cl- 425>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 426>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 427>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 428>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 429>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 430>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 431>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
For atom: .R<Cl- 432>.A<Cl- 1> Could not find vdW (or other) parameters for
type: Cl-
Parameter file was not saved.
For this reason I used $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff99SB, but in
these libraries there is not parameters for Calcium,
When I use ff14SB there is parameters for CO. If I check CO, it is OK, the
charge is +2.000, everything looks well, but when I try to save amberparms
I get messages above.
Thanks a lot for your help.
Regards
El abr 12, 2015 9:53 PM, "David A Case" <case.biomaps.rutgers.edu> escribió:
> On Sun, Apr 12, 2015, Carlos Romero wrote:
> >
> > The calcium.frcmod is:
> >
> > carlos.carlos-HP-G42-Notebook-PC:~/amber14/bin$ cat ioncalcio.frcmod
> > remark goes here
> > MASS
> > Co2+ 0.000 0.000 ATTN, need revision
> >
> > BOND
> >
> > ANGLE
> >
> > DIHE
> >
> > IMPROPER
> >
> > NONBON
> > Co2+ 0.0000 0.0000 ATTN, need revision
>
> OK: you should use the Ca+2 ions defined in atomic_ions.lib: antechamber
> won't
> help you here (it is for organic molecules). If you used the frcmod file
> above, nothing good could happen, since you have zero vdW parameters for
> your
> ion.
>
> ....dac
>
>
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>
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Received on Sun Apr 12 2015 - 20:30:02 PDT
