[gmx-users] gromacs energy minimization fatal error: Invalid bond type 1000 in constant-PH MD

[Mark Abraham]

Hi,

The number 1000 is suspiciously like a force constant someone would use for
position restraints, but somehow misnamed. Clearly the problem is external
to the fragment you shared, however.

Mark

On Thu, May 26, 2016 at 2:58 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/25/16 9:21 AM, Wang Tao wrote:
> > Hi,Dr Justin!
> >
> > You have mentioned that i missed my itp file.Here is it
> > ##########
> > <oh.itp>
> > [ moleculetype ]
> > ;molname    nrexcl
> >  OHIN          1
> >
> > [ atoms ]
> > ;id  at type  res nr  residue name at name cg nr charge mass
> > 1    opls_434     1        OHIN       OH      1   -1.300  15.999
> > 2    opls_435     1        OHIN       HO      2    0.300  1.008
> >
> > [ bonds ]
> > ;i j funct length    force.c
> >  1 2  1     0.09450  462750.4;
> > ##########
> > As you can see, that is how i defined the itp file of OH-.
> >
> > Those parameters can be found in oplsaa.ff/ffbonded.itp and
> oplsaa.ff/ffnonbonded.itp files.They have been provided in gromacs version
> 4.6.7.
> > Here are they:
> > ##########
> > <ffbonde.itp>
> > HO    OH      1    0.09450   462750.4   ; SUG(OL) wlj mod 0.96-> 0.945
> > ##########
> > <ffnonbonded.itp>
> >  opls_434   OH   8  15.99940    -1.300       A    3.20000e-01
> 1.04600e+00
> >  opls_435   HO   1   1.00800     0.300       A    0.00000e+00
> 0.00000e+00
> > ##########
> > But i really don't understand why the bond in OH- is invalid.Or in
> another word,what can i do to finish an sucessful energy minimization with
> OH- in my system?
> >
>
> No idea; it works for me.  I built a system of one OH- in vacuo, applied
> your
> topology, and it worked fine.  Probably something in the .top is broken,
> and
> #include statement in the wrong place or something else.
>
> -Justin
>
> > You also said that waht i am conduncting is not a true constant PH
> MD.Yes,you are right.I did have some misunderstanding about it. But in my
> system ,i intended to create an environment where there is plenty of
> OH-with fixed concentration of it.So fixed protonation  is ok in this work.
> But anyway, i am very interested in constant-PH MD,and want to do something
> about it.I would spend more time on it.
> >
> > Now,would you please offer me some advice on solve my problem above?
> >
> > Tao Wang
> >
> > Thank You!
> >
> >
> > Message: 2
> > Date: Wed, 25 May 2016 07:04:59 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] gromacs energy minimization fatal error:
> >         Invalid bond type 1000 in constant-PH MD
> > Message-ID: <fe760a05-25f0-7190-0003-139be796e0ee at vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 5/25/16 6:06 AM, Wang Tao wrote:
> >> Hi,every one!
> >>
> >> I'm using opls aa in gromacs to conduct constant-PH MD. In my system,PH
> is equal to 13.There are three kind of groups, NA+,OH- and H2O. The itp
> file for OH- is created by myself.
> >>
> >
> > This is not what constant pH MD is.  You've got a fixed protonation
> state with
> > OH- floating around, which may not be physically realistic.
> >
> >> After having finished the genbox and genion steps sucessfully, i met a
> problem in energy minimization step. The output information says:Invalid
> bond type 1000. But i don't really understand what the exact problem is.
> >>
> >>
> >> Tried to remove bond definition in itp file for OH-, don't work.
> >>
> >> Tried to remove bond definition in ffbonded.itp for OH-, don't work.
> >>
> >> Replaced OH- with CL-,error infomation disappeared.
> >>
> >>
> >> I believe the problem is related to OH- force field parameters,but
> don't know how to deal with it.
> >>
> >
> > You haven't provided us with its topology, so there's nothing anyone can
> do but
> > guess haphazardly.  But if removing it solves the problem, you know
> exactly
> > where the issue is.
> >
> > -Justin
> >
> >>
> >> Can anyone help me?
> >>
> >>
> >> Tao Wang
> >>
> >> Thank You!
> >>
> >
> > --
> > ==================================================
> >
> > 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
> >
> > ==================================================
> >
> >
> >
>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
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