[gmx-users] Re: gmx-users Digest, Vol 46, Issue 56
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 19 12:12:28 CET 2008
Quoting sudheer babu <sudheer.pbm07 at gmail.com>:
> Thanks Mark for your valuable reply and suggestions. If once i use "grompp"
> command its not showing any specific atom, its showing generally atomtype NR
> , HC, CR1 not found.
> if we come to topic of forcefields, For lipids i didnt use any Force field
> due to popc.top and popc.itp files downloaded from Peter tielman
> website and incase of my protein i have used "GROMOS96 43a1 force field".
> Pls help me.....
> Thanks in advance.....
Your problem is that you have blindly copied a topology file from online,
without giving any thought to what you're actually including :) I assume you
have copied the example topology from Peter Tieleman's site, which was created
long ago, probably when ffgmx was still considered useful. Try looking at the
original topology generated by pdb2gmx to see which force field should be
included.
-Justin
>
> On Feb 19, 2008 12:51 PM, <gmx-users-request at gromacs.org> wrote:
>
> > Send gmx-users mailing list submissions to
> > gmx-users at gromacs.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > or, via email, send a message with subject or body 'help' to
> > gmx-users-request at gromacs.org
> >
> > You can reach the person managing the list at
> > gmx-users-owner at gromacs.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: Lennard Jones spheres (Mark Abraham)
> > 2. Re: Proline on OPLSSaa (Mark Abraham)
> > 3. Re: problem regarding .top file generated by genbox (Mark Abraham)
> > 4. RE:problem regarding .top file generated by genbox (sudheer babu)
> > 5. Re: RE:problem regarding .top file generated by genbox
> > (Mark Abraham)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 19 Feb 2008 11:12:04 +1100
> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
> > Subject: Re: [gmx-users] Lennard Jones spheres
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <47BA1ED4.7050201 at anu.edu.au>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Chiara Parravicini wrote:
> > > Hi gromacs users,
> > >
> > > I would like to add LJ spheres into the protein cavitities, but I don't
> > > know how to define input parameters and files to set the run. Should I
> > > define spheres as "dummy atoms"? Any suggestion will be greatly
> > appreciated!
> >
> > How do you want these spheres to interact with the system?
> >
> > Mark
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Tue, 19 Feb 2008 11:13:41 +1100
> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
> > Subject: Re: [gmx-users] Proline on OPLSSaa
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <47BA1F35.1020001 at anu.edu.au>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Mauro Puppett wrote:
> > > -----------------------------
> > >
> > > Sorry but I'm not able to solve the problem.
> > > I've added the impropers for ACE and PRO but I still have warnings.
> > > Checking the lines, the warning refers to the dihedrals of the methoxy
> > group. I'm not able to find anywhere how to fix this problem.
> > > Could you please help me again?
> >
> > Probably, your force field doesn't have dihedrals for methoxy. You'll
> > have to parametrize yourself, or search the literature for others who
> > might have done it. Check out
> > http://wiki.gromacs.org/index.php/Parameterization
> >
> > Mark
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Tue, 19 Feb 2008 11:15:42 +1100
> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
> > Subject: Re: [gmx-users] problem regarding .top file generated by
> > genbox
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <47BA1FAE.2040904 at anu.edu.au>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Justin A. Lemkul wrote:
> > > I suspect you have an error with the order that you have included the
> > relevant
> > > .itp files within your topology. It would be helpful to include a
> > snapshot of
> > > your topology which illustrated the order in which these files are
> > included.
> > >
> > > Also, if you are asking whether your commands are right or not, you
> > should
> > > include your actual commands, otherwise our default assumption is
> > "probably
> > > not." :-)
> >
> > Yep, and also the OP didn't say what force field they were using. Since
> > this defines the atom types, and their problem was with unknown atom
> > types, this information is important.
> >
> > Mark
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Tue, 19 Feb 2008 11:53:14 +0530
> > From: "sudheer babu" <sudheer.pbm07 at gmail.com>
> > Subject: [gmx-users] RE:problem regarding .top file generated by
> > genbox
> > To: gmx-users at gromacs.org
> > Message-ID:
> > <76de29310802182223o37bde3abi639d6e01b365671f at mail.gmail.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Thanks for your reply Mr.justin
> > i am sending the commands and .itp file sequence
> > the command i have used for protein insertion into membrane is
> > genbox -cs lipid.gro -cp protein.gro -p topol.top -o popc_protein.gro ,
> > this
> > command was fine it ran without error.
> > Later
> > grompp -f em.mdp -c popc_protein.gro(generated by genbox) -p
> > topol.top(generated by genbox) -o
> > em.tpr
> > when i ran this grompp command its showing that atom typr NR, HC, CR1 not
> > found
> > i am pasting part of my topology file
> >
> > This is your topology file
> > ; "Move Over Hogey Bear" (Urban Dance Squad)
> > ;
> > ; Include forcefield parameters
> > #include "ffgmx.itp"
> > #include "lipid.itp"
> > #include "popc.itp
> >
> >
> > 17 N 3 HISH N 7 -0.28 14.0067 ; qtot
> > 0.72
> > 18 H 3 HISH H 7 0.28 1.008 ;
> > qtot
> > 1
> > 19 CH1 3 HISH CA 8 0 13.019 ;
> > qtot
> > 1
> > 20 CH2 3 HISH CB 8 0 14.027 ;
> > qtot
> > 1
> > 21 C 3 HISH CG 9 -0.05 12.011 ;
> > qtot
> > 0.95
> > 22 NR 3 HISH ND1 9 0.38 14.0067 ;
> > qtot
> > 1.33
> > 23 H 3 HISH HD1 9 0.3 1.008 ;
> > qtot
> > 1.63
> > 24 CR1 3 HISH CD2 9 0 13.019 ;
> > qtot
> > 1.63
> > 25 CR1 3 HISH CE1 9 -0.24 13.019 ;
> > qtot
> > 1.39
> > 26 NR 3 HISH NE2 9 0.31 14.0067 ;
> > qtot
> > 1.7
> > 27 H 3 HISH HE2 9 0.3 1.008 ;
> > qtot
> > 2
> > 28 C 3 HISH C 10 0.38 12.011 ;
> > qtot
> > 2.38
> > 29 O 3 HISH O 10 -0.38 15.9994 ;
> > qtot
> > 2
> > 30 N 4 HISH N 11 -0.28 14.0067 ;
> > qtot
> > 1.72
> > 31 H 4 HISH H 11 0.28 1.008 ;
> > qtot
> > 2
> > 32 CH1 4 HISH CA 12 0 13.019 ;
> > qtot
> > 2
> > 33 CH2 4 HISH CB 12 0 14.027 ;
> > qtot
> > 2
> > 34 C 4 HISH CG 13 -0.05 12.011 ;
> > qtot
> > 1.95
> > 35 NR 4 HISH ND1 13 0.38 14.0067 ;
> > qtot
> > 2.33
> > 36 H 4 HISH HD1 13 0.3 1.008 ;
> > qtot
> > 2.63
> > 37 CR1 4 HISH CD2 13 0 13.019 ;
> > qtot
> > 2.63
> > 38 CR1 4 HISH CE1 13 -0.24 13.019 ;
> > qtot
> > 2.39
> > 39 NR 4 HISH NE2 13 0.31 14.0067 ;
> > qtot
> > 2.7
> > 40 H 4 HISH HE2 13 0.3 1.008 ;
> > qtot
> > 3
> > 41 C 4 HISH C 14 0.38 12.011 ;
> > qtot
> > 3.38
> > 42 O 4 HISH O 14 -0.38 15.9994 ;
> > qtot
> > 3
> >
> > 366 N 41 PHE N 160 -0.28 14.0067 ; qtot
> > 2.72
> > 367 H 41 PHE H 160 0.28 1.008 ;
> > qtot
> > 3
> > 368 CH1 41 PHE CA 161 0 13.019 ;
> > qtot
> > 3
> > 369 CH2 41 PHE CB 161 0 14.027 ;
> > qtot
> > 3
> > 370 C 41 PHE CG 161 0 12.011 ;
> > qtot
> > 3
> > 371 C 41 PHE CD1 162 -0.1 12.011 ;
> > qtot
> > 2.9
> > 372 HC 41 PHE HD1 162 0.1 1.008 ;
> > qtot
> > 3
> > 373 C 41 PHE CD2 163 -0.1 12.011 ;
> > qtot
> > 2.9
> > 374 HC 41 PHE HD2 163 0.1 1.008 ;
> > qtot
> > 3
> > 375 C 41 PHE CE1 164 -0.1 12.011 ;
> > qtot
> > 2.9
> > 376 HC 41 PHE HE1 164 0.1 1.008 ;
> > qtot
> > 3
> > 377 C 41 PHE CE2 165 -0.1 12.011 ;
> > qtot
> > 2.9
> > 378 HC 41 PHE HE2 165 0.1 1.008 ;
> > qtot
> > 3
> > 379 C 41 PHE CZ 166 -0.1 12.011 ;
> > qtot
> > 2.9
> > 380 HC 41 PHE HZ 166 0.1 1.008 ;
> > qtot
> > 3
> > 381 C 41 PHE C 167 0.38 12.011 ;
> > qtot
> > 3.38
> > 382 O 41 PHE O 167 -0.38 15.9994 ;
> > qtot
> > 3
> >
> > ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre.itp"
> > #endif
> >
> > ; Include water topology
> > #include "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 generic topology for ions
> > #include "ions.itp"
> >
> > [ system ]
> > ; Name
> > protein in popc in water
> >
> > [ molecules ]
> > ; Compound #mols
> > Protein 1
> > POPC 98
> > CL- 3
> > SOL 2457
> > Thanks in advance.
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
>
http://www.gromacs.org/pipermail/gmx-users/attachments/20080219/b958713a/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Tue, 19 Feb 2008 18:20:55 +1100
> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
> > Subject: Re: [gmx-users] RE:problem regarding .top file generated by
> > genbox
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <47BA8357.5000609 at anu.edu.au>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > sudheer babu wrote:
> > > Thanks for your reply Mr.justin
> > > i am sending the commands and .itp file sequence
> > > the command i have used for protein insertion into membrane is
> > > genbox -cs lipid.gro -cp protein.gro -p topol.top -o popc_protein.gro ,
> > > this command was fine it ran without error.
> > > Later
> > > grompp -f em.mdp -c popc_protein.gro(generated by genbox) -p topol.top
> > > (generated by genbox) -o em.tpr
> > > when i ran this grompp command its showing that atom typr NR, HC, CR1
> > > not found
> > > i am pasting part of my topology file
> >
> > This is very hard to read. English uses capitalization of names and
> > first words in sentences, and punctuation, all to increase readability.
> > People are trained to read text where this occurs, and if you do not do
> > it then people find your work hard to read. They might well give up on
> > reading it, and when you're looking for free help, that's the last thing
> > you want to do!
> >
> > When moving in and out of English (into say, quoting GROMACS commands)
> > then you should indicate this with quotation marks "grompp -f em.mdp..."
> > , or starting new paragraphs:
> >
> > grompp -f em.mdp ...
> >
> > Yes, this is more work for you, however not doing that work is a false
> > economy - you lose people who don't bother to read your post at all.
> >
> > > This is your topology file
> > > ; "Move Over Hogey Bear" (Urban Dance Squad)
> > > ;
> > > ; Include forcefield parameters
> > > #include "ffgmx.itp"
> >
> > This force field is deprecated. That means you shouldn't be using it
> > without a sound reason. It also doesn't define the atom types that
> > grompp is complaining about. I guess that you did pdb2gmx on your
> > protein with one of the ffGxxx forcefields and are now mixing force
> > fields. DON'T! See http://wiki.gromacs.org/index.php/Force_Fields and
> > links thereon.
> >
> > > [ molecules ]
> > > ; Compound #mols
> > > Protein 1
> > > POPC 98
> > > CL- 3
> > > SOL 2457
> >
> > Don't do this either... see http://wiki.gromacs.org/index.php/Thermostats
> >
> > Mark
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> >
> > End of gmx-users Digest, Vol 46, Issue 56
> > *****************************************
> >
>
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
More information about the gromacs.org_gmx-users
mailing list