Dear Friends,
Does anybody know if there is a free program with gui to restore the coordinates of a short missing loop in a single protein chain. There are only 5 residues in the loop and the sequence of the loop is known. If your answer is based on Gromacs MD simulations then be verbouse, please.
Try ModLoop: https://modbase.compbio.ucsf.edu/modloop/
It's a free server. There's no GUI, but usually loop reconstruction and homology modeling programs are not based on GUIs.
Thank you, Dr. Justin, see you on gmx-users mailing list. Regards, NS
personally,for this kind of job, i'm using modeller V 9.14 with chimera.
Thank you dear Lionel Nauton , I have already downloaded and am trying Modeller 9.14
And you can try also also Rosetta, it has a cuple of implemented methods for loop reconstruction:
https://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_loop.html
Thank you all. I made the job on ModLoop: https://modbase.compbio.ucsf.edu/modloop/, as was suggested by Dr.Lemkul, followed by two short minimisation with nstlist=1.4 (first with emtol=1000,0 and the second with emtol parameter 100.0 KJ / mol by Gromacs (Amber 3) and results seem to be qite nice. Thank you all, who helped. Regatds
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