You may add new atom types to the PARMCHK.DAT file, for example:
PARM C8 0 0 12.01 0 6
EQUA CT
PARM CX 0 0 12.01 0 6
EQUA CT
put those lines immediately before the lines for weights:
-----------------------------
# weights of calculating penalty scores
All the best
Junmei
On Tue, Nov 20, 2018 at 11:47 AM Jaime Rubio Martinez <jaime.rubio.ub.edu>
wrote:
> Hello,
>
>
> Using ff14SB fforce field the ARG CA atom has CX atom type
>
> and atoms CB,CG and CD have C8 atom type.
>
> However parmchk2 program produce an error :
>
>
> Atom types C8 and CX are not in PARMCHK.dat
>
> ( also they do not have mass ..)
>
>
> How can I solve this problem ?
>
>
>
> ________________________________
> De: David Case <david.case.rutgers.edu>
> Enviat el: dijous, 15 de novembre de 2018 14:41:30
> Per a: AMBER Mailing List
> Tema: Re: [AMBER] Antechamber with protonated arginine
>
> On Thu, Nov 15, 2018, Jose Manuel Granadino Roldán wrote:
> >
> > I want to obtain parameters to simulate arginine fully protonated
> > (i.e. all protonable side chain and backbone atoms). I thought that
> > an option could be to use antechamber with the “-at amber” option but
> > I am not sure how it works. My guess is that after using that option,
> > if later on I use the ff99SB forcefield with Leap (the -at amber
> > option is said to work with that version of the force field), I would
> > end up using ff99SB force field parameters for standard arginine,
> > when possible, and antechamber generated parameters when not. Is
> > that correct? Could you give me any advise on how to obtain reliable
> > parameters?
>
> The "-at" switch just means that Amber atom types will be used (as much
> as possible) for the calculation. After you parmchk2, you will be able
> to see which parameters are being added to the "standard" ones in the
> force field.
>
> Here's perhaps a more understandable option, since you are just adding
> protons in various places: First, use resp to get the charge distribution
> (it
> won't matter what atom types are used for this step; you might want to
> use the RED server for this.
>
> Second, use xleap to create a protonated unit, starting from ff14SB.
> Save that as a mol2 file, and manually edit the file to put your resp
> charges in there. See if tleap complains about any missing parameters.
>
> I recommed this because it ensures that the atom types will be
> compatible with ff14SB, rather than the more generic ff99SB parameters.
>
> ...hope this helps....dac
>
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Received on Tue Nov 20 2018 - 13:00:03 PST
