[gmx-users] force field
jalemkul at vt.edu
Sun Aug 9 19:05:17 CEST 2015
On 8/9/15 12:59 PM, mohammad r wrote:
> Thank you MaryamI want to use this force field in the first step of generating the topology file (pdb2gmx command in the force field shown after this command). Is it possible? and unfortunately I don't know how to find the necessary files of this force field. I searched a lot but I didn't succeed.
If the force field files haven't been created already (in this case, they
haven't) you have to convert the force field files from AMBER format to GROMACS
format. That's a pretty big undertaking if you're not well versed in the formats.
> I have another question, is it possible to acetylate or ammoniate a peptide with gromacs?
Anything is possible, provided you have parameters for such species.
> thank you, M.
> On Sunday, August 9, 2015 8:17 PM, Maryam Kowsar <maryam.kowsar at gmail.com> wrote:
> let me modify my previous message: in the g_x2top command, not grompp :-)
> On Sun, Aug 9, 2015 at 8:14 PM, Maryam Kowsar <maryam.kowsar at gmail.com> wrote:
> Hi Mohammad,
> Yes that's possible. You should just have the necessary files of your desired forcefield(.atp,.itp,...), and put them in a folder. in the grompp command just add -ff folder name. that's all! It will use your forcefield instead of the present forcefields in gromacs.
> On Sun, Aug 9, 2015 at 5:57 PM, mohammad r <mohammad.r0325 at yahoo.com> wrote:
> I want to use ff14SB Amberprotein force field. But it isn't included in the gromacs force fields list.Is it possible to use this force field? How can I add it in?Thank you, Mohammad.
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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