Custom Search
-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Fri, Apr 3, 2015 at 7:43 PM, Neha Gandhi <n.gandhiau.gmail.com> wrote: > Dear Ray, > > Thanks for the update. I reinstalled amber 14 yesterday and it > automatically applied the patches. However, mmpbsa still didn't like inp=2 > with radiopt=0. > > The irony is I had 2 years old installation of amber 12 (probably with > ambertools 1.3) which worked with my current system with inp =2. > > I look forward to hear from you regarding patches for amber 14. > > Many thanks, > Neha > On 04/04/2015 1:28 am, "Ray Luo, Ph.D." <ray.luo.uci.edu> wrote: > >> Hi Neha, >> >> If you are using the latest AmberTools, radiopt=0 should work with >> both inp=2 and inp=1. Have you patched all updates? I remember there >> were some inconsistencies between the master source tree and the >> released version last year. The updates should have brought the >> released version up to date. Let me know if you still cannot run it >> with the updated Amber14. >> >> All the best, >> Ray >> -- >> Ray Luo, Ph.D. >> Professor, >> Biochemistry, Molecular Biophysics, Chemical Physics, >> Chemical and Biomedical Engineering >> University of California, Irvine, CA 92697-3900 >> >> >> On Fri, Apr 3, 2015 at 8:34 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote: >> > Dear List, >> > >> > I have used ff12SB forcefield and I am trying to do MM-PBSA calculation. >> > >> > I tried changing atom types such from CI to C using parmed.py as per the >> > this post on the mailing list >> > http://archive.ambermd.org/201208/0074.html >> > >> > Once I got rid of this atomtype, MMPBSA complained about CB. I saw this >> > mailing list by Ray Luo >> > http://archive.ambermd.org/201409/0222.html >> > >> > I am using AMBER14 and I was wondering if any progress has been made in >> > this regards? I tried radiopt=0 but it didn't help with inp=2. >> > >> > Any help is appreciated. >> > >> > -- >> > Regards, >> > Dr. Neha S. Gandhi, >> > Curtin Research Fellow, >> > School of Biomedical Sciences, >> > Curtin University, >> > Perth GPO U1987 >> > Australia >> > LinkedIn >> > Research Gate >> > _______________________________________________ >> > AMBER mailing list >> > AMBER.ambermd.org >> > http://lists.ambermd.org/mailman/listinfo/amber >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Apr 03 2015 - 22:30:02 PDT