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 <jalem...@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 <jalem...@vt.edu> > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] gromacs energy minimization fatal error: > > Invalid bond type 1000 in constant-PH MD > > Message-ID: <fe760a05-25f0-7190-0003-139be796e...@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 > > > > jalem...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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? 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