[gmx-users] Increase the box size or decrease rlist
pragna lakshmi
pragnapcu at gmail.com
Wed Aug 20 18:56:38 CEST 2014
Thank you Mark for ur reply.
In the generated POPC.top from POPC.pdb and POPC.psf using VMD, the charges
have become to zero. Here are few lines of my POPC.top
[ atomtypes ]
; name bond_type mass charge ptype sigma epsilon
C1 C 1.0 0.0 A 0.0 0.0
C11 C 1.0 0.0 A 0.0 0.0
C12 C 1.0 0.0 A 0.0 0.0
C13 C 1.0 0.0 A 0.0 0.0
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 N 1 POPC N 1 0.0000 14.0070
2 C11 1 POPC C11 2 0.0000 12.0110
3 C12 1 POPC C12 2 0.0000 12.0110
4 C13 1 POPC C13 3 0.0000 12.0110
My question is whether this could be the reason for not having the charges
over the atoms.
If it is so, could you please suggest me the proper way of getting
parameters for POPC (charmm36 ff).
Thanking You,
On Wed, Aug 20, 2014 at 8:37 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> You can't have a sensible bilayer with atomistic water and have no charged
> atoms! Please reconsider however you are generating that input.
>
> Mark
>
>
> On Wed, Aug 20, 2014 at 4:33 PM, pragna lakshmi <pragnapcu at gmail.com>
> wrote:
>
> > I could solve the fatal error by giving box vectors 4.84331 4.84331
> 6.69130
> > while generating .gro file from .pdb using editconf.
> > Then, the following warning:
> > WARNING 1 [file minim.mdp]:
> > You are using full electrostatics treatment PME for a system without
> > charges.
> > This costs a lot of performance for just processing zeros, consider
> using
> > Cut-off instead.
> >
> >
> > So, should i give -maxwarn 1 or change the electrostatics from 'PME' to
> > 'Cut-off'. Can anyone please suggest?
> >
> > Thanking You,
> >
> >
> >
> > On Wed, Aug 20, 2014 at 8:55 AM, pragna lakshmi <pragnapcu at gmail.com>
> > wrote:
> >
> > > Thank u Justin for your reply.
> > > I have realized that stockholm lipids are derived from Amber ff. But i
> am
> > > unable to get parameters for POPC derived from charmm ff. Is there any
> > > source for that?
> > > The box vectors that are listed in POPC.gro are 0.00000 0.00000
> > > 0.00000
> > >
> > >
> > >
> > > On Tue, Aug 19, 2014 at 11:50 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > >
> > >>
> > >>
> > >> On 8/19/14, 2:14 PM, pragna lakshmi wrote:
> > >>
> > >>> Dear all,
> > >>> I am trying to do MD simulation of POPC membrane simulation with
> > >>> peripheral
> > >>> attachment of protein ligand complex. Steps that i have performed so
> > far
> > >>> are:
> > >>>
> > >>> 1. orienting the protein with editcong -princ command
> > >>> 2. rotating it along the y-axis with editconf -rotate 0 40 0 command
> > >>> 3. separation of protein ligand files into individual files and
> > >>> generation
> > >>> of topology file of protein from pdb2gmx and ligand from swissparam.
> > >>> (charmm 36ff was used for protein topology generation. source:
> > >>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs )
> > >>> 4. The protein and ligand files were merged followed by necessary
> > changes
> > >>> in topology file.
> > >>> 5. Pre-equilibrated POPC bilayer was downloaded from Dr.Klauda's
> > website
> > >>> whereas its itp file was taken from Stockholm_Lipids website.
> > >>>
> > >>
> > >> The Stockholm lipids are derived from Amber force fields. You can't
> > >> combine them with CHARMM protein parameters and expect anything
> > physically
> > >> meaningful. If you're using the CHARMM protein force field, use the
> > CHARMM
> > >> lipid parameters.
> > >>
> > >>
> > >> 6. After this, when i am running the command
> > >>> grompp -f minim.mdp -c POPC.gro -p POPC.top -o em_POPC.tpr
> > >>> i am facing the fatal error:
> > >>> ERROR: The cut-off length is longer than half the shortest box vector
> > or
> > >>> longer than the smallest box diagonal element. Increase the box
> size
> > >>> or
> > >>> decrease rlist.
> > >>>
> > >>
> > >> What are the box vectors listed in POPC.gro?
> > >>
> > >>
> > >> As it is suggesting, I have decreased rlist, rcoulomb and rvdw from
> 1.2
> > >>> to
> > >>> 1.0. But still the same error is raising.
> > >>>
> > >>
> > >> Don't mess with these settings just to make an error message go away.
> > >> The nonbonded setup is a fixed feature of the force field, and lipids
> > are
> > >> especially sensitive to changes here. I just posted the proper
> settings
> > >> for the CHARMM force field a few days ago; use those settings and
> don't
> > >> deviate unless you have proof that what you're doing is superior.
> > >>
> > >> -Justin
> > >>
> > >> --
> > >> ==================================================
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >>
> > >> Department of Pharmaceutical Sciences
> > >> School of Pharmacy
> > >> Health Sciences Facility II, Room 601
> > >> University of Maryland, Baltimore
> > >> 20 Penn St.
> > >> Baltimore, MD 21201
> > >>
> > >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > >> http://mackerell.umaryland.edu/~jalemkul
> > >>
> > >> ==================================================
> > >> --
> > >> Gromacs Users mailing list
> > >>
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> > >>
> > >
> > >
> > >
> > > --
> > > Pragna Lakshmi.T,
> > > Ph.D. Scholar,
> > > IPLS Project,
> > > Pondicherry University,
> > > Pondicherry,
> > > India - 605014.
> > >
> >
> >
> >
> > --
> > Pragna Lakshmi.T,
> > Ph.D. Scholar,
> > IPLS Project,
> > Pondicherry University,
> > Pondicherry,
> > India - 605014.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> >
> --
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--
Pragna Lakshmi.T,
Ph.D. Scholar,
IPLS Project,
Pondicherry University,
Pondicherry,
India - 605014.
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