Re: [AMBER] Antechamber with protonated arginine

From: Jaime Rubio Martinez <>
Date: Tue, 20 Nov 2018 16:47:34 +0000


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 <>
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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