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.
-Justin
thank you, M.
On Sunday, August 9, 2015 8:17 PM, Maryam Kowsar
<[email protected]> 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 <[email protected]> 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.
Regards,-Maryam
On Sun, Aug 9, 2015 at 5:57 PM, mohammad r <[email protected]> wrote:
Hi;
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.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to [email protected].
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to [email protected].
