The ATB generator does a reasonable job, but for some reason it gets some things wrong. If you can look at that topology, identify the problematic parts of it, see if that is consistent with the forcefield, and then if not adjust the parameters. Particularly I have found that some angles are way too large, giving fast moving bond angles, which then become unstable. Catch ya,
Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On 24 May 2018 at 22:01, <nik...@tezu.ernet.in> wrote: > Hello, > > I have tried doing the Molecular dynamics simulation of AMP using the > Gromos54a7 forcefield. > > ITP parameters for the AMP molecule has been generated using the ATB > builder. Minimization of the molecule goes on well however while carrying > out the Nvt theres a segmantation fault resulting in step files. > > Moreover LINCS warning are shown with bonds that rotated more than 30 > degrees. ihave tried changing lincs parameter and also increasing the step > size, but still simulation crashes. > > Is it suggestible to generate topology for the AMP molecule from the > available topological parameters of ATP in GROMACS. Or are their any > source of getting the correct itp paremeters for "AMP". > > Thanks > Nikita Bora > > > * * * D I S C L A I M E R * * * > This e-mail may contain privileged information and is intended solely for the > individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail in error and destroy > it from your system. Though considerable effort has been made to deliver > error free e-mail messages but it can not be guaranteed to be secure or > error-free as information could be intercepted, corrupted, lost, destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message. > -- > 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 gmx-users-requ...@gromacs.org. -- 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 gmx-users-requ...@gromacs.org.
