Thank you, Elvis for such a quick response. I just recreated new topology
files using t-leap as I typically do and GBSA is running fine. I just
wanted to make sure.
Thank you again. I really appreciate.
Jag
On Sun, Jun 25, 2017 at 8:18 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Hi,
>
> There is no need to re-run your simulations
>
> You can use parmed to assign mbondi3 radii and save new prmtop file.
>
>
> Best Regards
>
> [photo]
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
> Skype. adrian_elvis12<https://webapp.wisestamp.com/#>
>
>
> [https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-
> ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_
> yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-
> d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/
> icons_for_colors_32/linkedin.png]<http://www.linkedin.com/
> in/elvisadrianmartis/>
>
>
>
>
>
> ________________________________
> From: Jag Silwal <jagsilwal.gmail.com>
> Sent: 25 June 2017 17:15:15
> To: AMBER Mailing List
> Subject: [AMBER] mbondi set up
>
> Dear all,
>
> I just have a very trivial question. I just finished 200 ns simulation in
> my protein complex. But just when running MMGBSA, I realized that while
> saving the initial topology and coordinate files for everything, I forgot
> to set PBRadii mbondi. (I usually use "set default PBRadii mbondi3" just
> before saving solvated and non solvated topologies and coordinates). I
> completely missed this command in tleap. I came to realize this when
> prmtop failure message popped out during MMGBSA run.
>
> Now my question is do I need to re-run the entire simulation from the
> scratch (with mbondi) or can I simply create a new topology file with
> mbondi and use these to already ran simulation to do further analyses? As
> far as I understand, mbondi and igb are parameters for GB/SA run. I
> recreated the topology files using mbondi and I didn't get any errors
> while calculating MMGBSA.
>
> I just wanted to be 100% on this before I do anything with this.
>
> I would greatly appreciate your help.
>
>
> Sincerely,
>
> Jag Siwal
>
> Graduate Student
> Department of Chemistry
> Michigan State University
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Received on Sun Jun 25 2017 - 05:30:05 PDT
