[gmx-users] Re: gmx-users Digest, Vol 46, Issue 56
sudheer babu
sudheer.pbm07 at gmail.com
Tue Feb 19 09:39:19 CET 2008
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.....
On Feb 19, 2008 12:51 PM, <gmx-users-request at gromacs.org> wrote:
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> 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.
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> ------------------------------
>
> 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
>
>
> ------------------------------
>
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> End of gmx-users Digest, Vol 46, Issue 56
> *****************************************
>
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