Good day! My name is Sergei Vladimirov, I'm a student at Moscow State University. As far as I know, when running a molecular dynamics of ligand-protein interaction one must use different force fields to the ligand and the protein. There is a mm14ff to calculate interactions within a protein but there are only two different force fields to calculate interactions within a ligand. I've been led into believing that the best ff for small organic ligands is GAFF. So my question is, is there any way to implement the GAFF force field into the production of molecular dynamics? Is there anything I'm missing? I will be awaiting your reply. Best regards, Sergei Vladimirov.
Hi Sergei, It already is. That is, if your system includes a nonstandard residue like some ligand, then Chimera automatically uses Ambertools/Antechamber to generate GAFF parameters to use in minimization and/or dynamics. This is all described in the Minimize Structure manual page, see the section on "Force Field Parameters": <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2020, at 12:29 PM, Сергей Владимиров <sergei.vladimirov@chemistry.msu.ru> wrote:
Good day!
My name is Sergei Vladimirov, I'm a student at Moscow State University. As far as I know, when running a molecular dynamics of ligand-protein interaction one must use different force fields to the ligand and the protein. There is a mm14ff to calculate interactions within a protein but there are only two different force fields to calculate interactions within a ligand. I've been led into believing that the best ff for small organic ligands is GAFF. So my question is, is there any way to implement the GAFF force field into the production of molecular dynamics?
Is there anything I'm missing? I will be awaiting your reply.
Best regards, Sergei Vladimirov.
Good day! Sorry for the late reply. Yes, I read this article but what confuses me is that during the minimisation steps I'm offered two possible ff for a ligand -- AM1-BCC and Gasteiger. So, basically what you are saying is that both atom charges and atom types are assigned using GAFF, not AM1-BCC? Could you explain that in a little more detail? For example, here ( http://ambermd.org/antechamber/ac.html#atomtype) it says that an atom type in antachamber might be assigned either by GAFF or by AM1-BCC or by other ff. And do I understand correctly that within antachamber there are only two possible ways to assign charge and those are AM1-BCC and Gasteige? Correct me if I misunderstood you. Best regards, Sergey Vladimirov. On Sat, May 23, 2020 at 12:47 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Sergei, It already is. That is, if your system includes a nonstandard residue like some ligand, then Chimera automatically uses Ambertools/Antechamber to generate GAFF parameters to use in minimization and/or dynamics.
This is all described in the Minimize Structure manual page, see the section on "Force Field Parameters": < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize....
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2020, at 12:29 PM, Сергей Владимиров < sergei.vladimirov@chemistry.msu.ru> wrote:
Good day!
My name is Sergei Vladimirov, I'm a student at Moscow State University. As far as I know, when running a molecular dynamics of ligand-protein interaction one must use different force fields to the ligand and the protein. There is a mm14ff to calculate interactions within a protein but there are only two different force fields to calculate interactions within a ligand. I've been led into believing that the best ff for small organic ligands is GAFF. So my question is, is there any way to implement the GAFF force field into the production of molecular dynamics?
Is there anything I'm missing? I will be awaiting your reply.
Best regards, Sergei Vladimirov.
Hi Sergey, The partial atomic charges are calculated by the AM1-BCC method or Gasteiger method, as specified by you. The other parameters are GAFF. GAFF does not include include charges.
This is all described in the Minimize Structure manual page, see the section on "Force Field Parameters": <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>
" Minimize Structure uses the GAFF types to associate nonstandard residues with parameters other than charges." I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 31, 2020, at 12:54 PM, Сергей Владимиров <sergei.vladimirov@chemistry.msu.ru> wrote:
Good day!
Sorry for the late reply. Yes, I read this article but what confuses me is that during the minimisation steps I'm offered two possible ff for a ligand -- AM1-BCC and Gasteiger. So, basically what you are saying is that both atom charges and atom types are assigned using GAFF, not AM1-BCC?
Could you explain that in a little more detail? For example, here (http://ambermd.org/antechamber/ac.html#atomtype) it says that an atom type in antachamber might be assigned either by GAFF or by AM1-BCC or by other ff. And do I understand correctly that within antachamber there are only two possible ways to assign charge and those are AM1-BCC and Gasteige?
Correct me if I misunderstood you.
Best regards, Sergey Vladimirov.
On Sat, May 23, 2020 at 12:47 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Sergei, It already is. That is, if your system includes a nonstandard residue like some ligand, then Chimera automatically uses Ambertools/Antechamber to generate GAFF parameters to use in minimization and/or dynamics.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2020, at 12:29 PM, Сергей Владимиров <sergei.vladimirov@chemistry.msu.ru> wrote:
Good day!
My name is Sergei Vladimirov, I'm a student at Moscow State University. As far as I know, when running a molecular dynamics of ligand-protein interaction one must use different force fields to the ligand and the protein. There is a mm14ff to calculate interactions within a protein but there are only two different force fields to calculate interactions within a ligand. I've been led into believing that the best ff for small organic ligands is GAFF. So my question is, is there any way to implement the GAFF force field into the production of molecular dynamics?
Is there anything I'm missing? I will be awaiting your reply.
Best regards, Sergei Vladimirov.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Elaine Meng -
Сергей Владимиров