> > Message: 1 > Date: Thu, 21 Mar 2013 07:05:44 -0400 > From: Justin Lemkul <[email protected]> > Subject: Re: [gmx-users] Restraining water molecule > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 3/21/13 4:29 AM, neeru sharma wrote: > >> Message: 6 > >> Date: Wed, 20 Mar 2013 09:04:05 -0400 > >> From: Justin Lemkul <[email protected]> > >> Subject: Re: [gmx-users] Restraining water molecule > >> To: Discussion list for GROMACS users <[email protected]> > >> Message-ID: > >> < > >> caduqwc5+fotchpmi0pqeexcnpkbtqa-yb0px1p889gy3jza...@mail.gmail.com> > >> Content-Type: text/plain; charset=ISO-8859-1 > >> > >> On Wed, Mar 20, 2013 at 8:57 AM, neeru sharma <[email protected] > >>> wrote: > >> > >>> Dear gromacs users, > >>> > >>> I am simulating a system of Protein-ion-GTP with One Water molecule. I > >> want > >>> to restrain this system (along with this water molecule) for > minimization > >>> and equilibration. > >>> > >>> Everytime I run this by specifying the .itp files, it gives the error > of > >>> misplacement as follows: > >>> > >>> *"This probably means that you have inserted topology section > >>> "position_restraints" > >>> in a part belonging to a different molecule than you intended to. > >>> In that case move the "position_restraints" section to the right > >> molecule." > >>> * > >>> > >>> The sequence I am giving in the topology file is like this: > >>> > >>> > >>> > >>> * > >>> ; Include Position restraint file for Protein-ion-GTP-Water > >>> #ifdef POSRES_LIGAND > >>> #include "posre_comp.itp" > >>> #endif > >>> > >>> ; Include ligand topology > >>> #include "gtp.itp" > >>> > >>> ; Include water topology > >>> #include "gromos43a1.ff/spc.itp" > >>> > >>> > >>> > >>> #ifdef POSRES_WATER > >>> ; Position restraint for each water oxygen > >>> [ position_restraints ] > >>> ; i funct fcx fcy fcz > >>> 1 1 1000 1000 1000 > >>> #endif > >>> > >>> ; Include topology for ions > >>> #include "gromos43a1.ff/ions.itp"* > >>> * > >>> > >>> [ system ] > >>> ; Name > >>> Protein in water > >>> > >>> [ molecules ] > >>> ; Compound #mols > >>> Protein 1 > >>> GTP 1 > >>> SOL 1 > >>> SOL 12179 > >>> NA 8 > >>> * > >>> > >>> Can anybody help me figuring out the issue,where I am doing wrong? Any > >>> suggestion is welcome > >>> > >>> > >> If you want to restrain a single water molecule, it needs to be defined > as > >> its own [moleculetype] or as a part of the protein [moleculetype]. > Breaking > >> apart a continuous block of water causes problems with the SETTLE > >> algorithm, so you will need to manually specify three constraints > (OW-HW1, > >> OW-HW2, and HW1-HW2) for this water molecule, while the remaining bath > of > >> solvent would be handled by SETTLE. > >> > >> -Justin > >> > >> -- > >> > >> ======================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Research Scientist > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) > >> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >> > >> ======================================== > >> > >> > >> ------------------------------ > >> > >> -- > >> gmx-users mailing list > >> [email protected] > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> > >> End of gmx-users Digest, Vol 107, Issue 81 > >> ****************************************** > >> > > > > I tried restraining the single water molecule by specifying the > > Protein-Ion-GTP-Water as one index group. The itp file, I used for this > > water molecule was as follows: > > > > > > *[ moleculetype ] > > ; molname nrexcl > > WAT 2 > > > > [ atoms ] > > ; nr type resnr residue atom cgnr charge mass > > #ifndef HEAVY_H > > 1 O 1 WAT O 1 -0.82 15.99940 > > 2 H 1 WAT H1 1 0.41 1.00800 > > 3 H 1 WAT H2 1 0.41 1.00800 > > #else > > 1 O 1 WAT O 1 -0.82 9.95140 > > 2 H 1 WAT H1 1 0.41 4.03200 > > 3 H 1 WAT H2 1 0.41 4.03200 > > #endif > > > > #ifndef FLEXIBLE > > [ settles ] > > ; O funct doh dhh > > 1 1 0.1 0.16330 > > > > [ exclusions ] > > 1 2 3 > > 2 1 3 > > 3 1 2 > > #else > > [ bonds ] > > ; i j funct length force.c. > > 1 2 1 0.1 345000 0.1 345000 > > 1 3 1 0.1 345000 0.1 345000 > > > > [ angles ] > > ; i j k funct angle force.c. > > 2 1 3 1 109.47 383 109.47 383 > > #endif* > > > > > > > > But, ended with the fatal error: > > > > > > *Fatal error: > > The [molecules] section of your topology specifies more than one block of > > a [moleculetype] with a [settles] block. Only one such is allowed. If you > > are trying to partition your solvent into different *groups* (e.g. for > > freezing, T-coupling, etc.) then you are using the wrong approach. Index > > files specify groups. Otherwise, you may wish to change the least-used > > block of molecules with SETTLE constraints into 3 normal constraints.* > > > > > > > > Then, I tried removed the settles block: > > > > *[ settles ] > > ; O funct doh dhh > > 1 1 0.1 0.16330 > > > > *from the itp file. It then, ran the minimization steps which continued > for > > 40 steps. But when I visualized the gro file generated, the conformation > > and orientation of this particular water molecule was not proper. I > feel, I > > the settle section of itp file was not treated properly. > > > > Any suggestion how to treat this water molecule? > > > > Yes, read my post again. I already said this would happen and described > exactly > what you have to do. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > Dear Justin,
I understood the fact that settle can not be applied more than once. I removed the settle section from the itp file file, but I am still unable to get how to apply restraint to OW-HW1,OW-HW2 and HW1-HW2 and where to include these restraints, either in the protein's itp file or a separate .itp file for this water molecule. --Neeru -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
