[gmx-users] LINCS warnings and ligand topology

[Justin Lemkul]

On 5/11/15 9:07 PM, MPI wrote:
> Hi Justin,
>
> Thanks for your suggestions.
>> Hacking off atoms because the simulation fails is a pretty bad strategy :)
>
> Indeed, I removed all O atoms and S atom.  Simulations in solvent are
> perfectly fine. This might suggest  that  the errors (warnings) came
> directly from these deleted atoms, especially O3 indexed 2073.
> 131DRG     O3 2073   1.789   5.047   4.061
>
>> It could also be a problem with your protocol and/or .mdp files, but only by
>> systematically investigating what's going on will you figure out what the
>> problem is.
>
> The input mdp files are from your protein-lignad (JZ4) tutorial and
> they work well with various (many other) ligands in other proteins
> (systems in solvent) . However, this O3 atom 2073 with H  causes LINCS
> warnings.
>

Be advised that the tutorial .mdp settings are for GROMOS force fields; if 
you're using other force fields, those settings are wrong...

> Also, I  tried  EM  for this ligand in vacuum and MD production in
> vacuum.  It turns out  the system  of this ligand  only   is NOT
> stable because of warnings as below.  It usually  dose not happen in
> other ligands like JZ4.
>

If the ligand in vacuum is not stable, then your topology is bad and requires 
better parametrization.

-Justin

>
> ############################
> WARNING: Listed nonbonded interaction between particles 6 and 50
> at distance 3f which is larger than the table limit 3f nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
>
> ############################
>
> Again,  is there a way to fix this ligand topology generated by prodrg
> /Acpype because both methods have the same/similar output ?   The mdp
> files in vacuum are attached.
>
>
> Thanks,
>
> Dewey
>
>
>
> #em.mdp   in vaccum
>
> cpp                      = /usr/bin/cpp
> define                   = -DFLEXIBLE
> integrator               = steep
> nsteps                   = 5000
> constraints              = none
> emtol                    = 100.0
> emstep                   = 0.01
> nstcomm                  = 1
> ns_type                  = simple
> nstlist                  = 0
> rlist                    = 0
> rcoulomb                 = 0
> rvdw                     = 0
> Tcoupl                   = no
> Pcoupl                   = no
> gen_vel                  = no
> nstxout                  = 1
> pbc                      = no
>
> # md.mdp  in vacuum
>
> cpp                      = /usr/bin/cpp
> define                   = ;-DFLEXIBLE
> integrator               = md
> nsteps                   = 50000
> constraints              = none
> emtol                    = 100.0
> emstep                   = 0.01
> comm_mode                = angular
> ns_type                  = simple
> nstlist                  = 0
> rlist                    = 0
> rcoulomb                 = 0
> rvdw                     = 0
> Tcoupl                   = no
> Pcoupl                   = no
> gen_vel                  = no
> nstxout                  = 1
> pbc                      = no
>

-- 
==================================================

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================