Dear Vsevolod,
since you intend to create a new residue, you have to ensure that it has
the correct atom types for the new topology, adapted (newly generated)
atomic charges, and all necessary parameters, which arise from the atom
types and the topology.
Since you obviously want to apply parm19SB, I have no solution for you
out of the box. For parm14SB and parm99SB I had a parameter set ready to
use, which I could share with you (and which still awaits its due
publication, alas ...)
Concerning the order of reading in parameters:
As a rule of thumb, read in any modified parameters after the respective
general parameters have been read in, because the special parameters
normally build on the general ones; and solvent parameters normally go last.
Maybe this helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 08/18/2023 06:17 PM, amber--- via AMBER wrote:
> Dear Amber community,
>
> I'm trying to figure out how LEaP concepts work. Please, check the script I wrote to build isolysine residue (lysine which forms amide bond with ε-N-atom), is it correct? I will really appreciate any help
> source leaprc.protein.ff19SB
> source leaprc.gaff
>
> LYX = copy LYS
> set LYX name "LYX"
> set LYX.1 name "LYX"
>
> # terminal nytrogen
> set LYX.1.NZ type n3
> set LYX head LYX.1.NZ
> set LYX.1 connect0 LYX.1.NZ
>
> # terminal hydrogens
> remove LYX LYX.1.HZ3
> set LYX.1.HZ1 type hn
> set LYX.1.HZ2 type hn
>
> # build peptide
> p = sequence { ALA LYX ALA LYS }
> Also I have a question: I've found in the documentation that water parameters must be sourced after macromolecular parameters, in which order must I source custom and GAFF parameters?
> — Vsevolod
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Received on Sat Aug 19 2023 - 04:00:02 PDT
