On 01/25/11, ahmet yıldırım <[email protected]> wrote: > Dear Mark, > > A million thanks. Problem is solved. > Finally, > Select a continuous group of solvent molecules: > ... > Group 12 ( Water) has 126219 elements > Group 13 ( SOL) has 126219 elements > > > Which one should I choose 12 or 13? >
They're probably the same. Mark > > > Final topol.top file: > > > ; File 'topol.top' was generated > ; By user: onbekend (0) > ; On host: onbekend > ; At date: Tue Jan 25 10:12:14 2011 > > ; > ; This is a standalone topology file > ; > ; It was generated using program: > ; pdb2gmx - VERSION 4.5.3 > ; > ; Command line was: > ; pdb2gmx -f 3MOA.pdb -water spc -ter > ; > ; Force field was read from the standard Gromacs share directory. > > ; > > ; Include forcefield parameters > #include "gromos43a1.ff/forcefield.itp" > > ; Include chain topologies > #include "topol_Protein_chain_P.itp" > #include "topol_Protein_chain_L.itp" > > #include "topol_Protein_chain_H.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 > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 > ANTIBODY 2F5 HEAVY CHAIN in water > > > [ molecules ] > ; Compound #mols > Protein_chain_P 1 > Protein_chain_L 1 > Protein_chain_H 1 > SOL 10 > SOL 127 > SOL 157 > SOL 41771 > > CL 8 > > > > 25 Ocak 2011 13:13 tarihinde Mark Abraham <[email protected]> yazdı: > > > > > > > > > On 01/25/11, ahmet yıldırım <[email protected]> wrote: > > > > > > > > Dear Mark and Emanuel, > > > > > > I am sending the ions.tip and the topol.top files. Everything seems ok. > > > Any problem about these files? > > > > > > > > > > > > No. So one of the other #include files is erroneously defining ion molecule > > types. See > > www.gromacs.org/Documentation/Include_File_Mechanism(http://www.gromacs.org/Documentation/Include_File_Mechanism). > > Go and read them and fix it. > > > > > > As the link I sent last time hinted, you need to name *molecules* in the > > [molecules] directive. Look carefully at the *molecule* name of chloride > > where it is defined. > > > > Mark > > > > > > > > > > > > > > > > > > By the way, I am using the Gromacs 4.5.3. > > > Force Field 43a1 > > > > > > 25 Ocak 2011 12:03 tarihinde Emanuel Peter > > > <[email protected]> yazdı: > > > > > > > > > > > > > Hello, > > > > > > > > You have to look into your ions.itp which is included in your top-file > > > > by #include ions.itp. > > > > > > > > > > > > There all the types of ions have to be defined. > > > > The atom-types which you can see in the ions.itp, you will > > > > find in the ff"your-forcefield".itp where your atomtypes are defined. > > > > On top of your .top file the Atomtype-itp-file is included. > > > > > > > > > > > > All these files are normally placed in /usr/share/gromacs/top/. > > > > But you also can place them into your current directory. > > > > > > > > Bests, > > > > > > > > Emanuel > > > > > > > > >>> Mark Abraham 25.01.11 10.48 Uhr >>> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 01/25/11, ahmet yıldırım <[email protected]> wrote: > > > > > > > > > > > > > > > Dear Mark, > > > > > > > > > > I looked at gromacs mail list but I could not find a proper solution > > > > > .What should I add to the .top file? Please look at the following > > > > > reconstructed1 .top and reconstructed1 .top files > > > > > > > > > > > > > > > > > > > > > > > > > I have error as the following reconstructed1 .top file: > > > > > > > > > > Fatal error: > > > > > > > > > > moleculetype CU1 is redefined > > > > > > > > > > > > > > > I have error as the following reconstructed2 .top file: > > > > > > > > > > Fatal error: > > > > > > > > > > No such moleculetype CL- > > > > > > > > > > > > > > > > > > I don't have any knowledge of the context, so can't answer. It looks to > > > > me like you are mixing copies of ions.itp from multiple sources. Don't. > > > > Use the one for the force field you are targetting. pdb2gmx generated > > > > the right invocation - all you should have to do is use that by > > > > generating correctly-named ions. See > > > > http://www.gromacs.org/Documentation/Gromacs_Utilities/genion(http://www.gromacs.org/Documentation/Gromacs_Utilities/genion) > > > > > > > > > > > > > > > > Mark > > > > > > > > > > > > > Original .top file: > > > > > ; Include topology for ions > > > > > #include "gromos43a1.ff/ions.itp" > > > > > > > > > > > > > > > > > > > > [ system ] > > > > > ; Name > > > > > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; > > > > > ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water > > > > > > > > > > > > > > > [ molecules ] > > > > > ; Compound #mols > > > > > Protein_chain_P 1 > > > > > Protein_chain_L 1 > > > > > Protein_chain_H 1 > > > > > SOL 10 > > > > > SOL 127 > > > > > SOL 157 > > > > > SOL 41779 > > > > > > > > > > > > > > > > > > > > > > > > > reconstructed1 .top file > > > > > ; Include topology for ions > > > > > #include "gromos43a1.ff/ions.itp" > > > > > #include "ions.itp" > > > > > > > > > > [ system ] > > > > > ; Name > > > > > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; > > > > > ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water > > > > > > > > > > > > > > > > > > > > > > > > > [ molecules ] > > > > > ; Compound #mols > > > > > Protein_chain_P 1 > > > > > Protein_chain_L 1 > > > > > Protein_chain_H 1 > > > > > SOL 10 > > > > > SOL 127 > > > > > SOL 157 > > > > > SOL 41771 > > > > > > > > > > > > > > > > > > > > CL- 8 > > > > > reconstructed2 .top file > > > > > ; Include topology for ions > > > > > #include "gromos43a1.ff/ions.itp" > > > > > > > > > > [ system ] > > > > > ; Name > > > > > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; > > > > > ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water > > > > > > > > > > > > > > > > > > > > > > > > > [ molecules ] > > > > > ; Compound #mols > > > > > Protein_chain_P 1 > > > > > Protein_chain_L 1 > > > > > Protein_chain_H 1 > > > > > SOL 10 > > > > > SOL 127 > > > > > SOL 157 > > > > > SOL 41771 > > > > > > > > > > > > > > > > > > > > CL- 8 > > > > > > > > > > > > > > > 25 Ocak 2011 10:49 tarihinde Mark Abraham <[email protected]> > > > > > yazdı: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On 01/25/11, ahmet yıldırım <[email protected]> wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > > In my simulation, total charge of the system is a noninteger > > > > > > > number (System has non-zero total charge: 8.000004e+00). I > > > > > > > neutralized it with 8 chlorine atoms. > > > > > > > Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Fatal error: > > > > > > > > > > > > > > moleculetype CU1 is redefined > > > > > > > is it some thing wrong? > > > > > > > > > > > > > > > > > > > > > > > > > ions.itp defines molecule types for ions. Molecule types cannot be > > > > > > redefined. When you #included ions.itp GROMACS thought you were > > > > > > doing illegal redefinitions. Look back in the .top to find the > > > > > > original definitions, and then take suitable action. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Mark > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Below is the first and final version of the .top file: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > First topol.top File > > > > > > > .... > > > > > > > [ molecules ] > > > > > > > ; Compound #mols > > > > > > > Protein_chain_P 1 > > > > > > > Protein_chain_L 1 > > > > > > > Protein_chain_H 1 > > > > > > > SOL 10 > > > > > > > SOL 127 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > SOL 157 > > > > > > > SOL 41779 > > > > > > > > > > > > > > > > > > > > > Final topol.top File > > > > > > > #include "ions.itp" > > > > > > > > > > > > > > [ molecules ] > > > > > > > ; Compound #mols > > > > > > > Protein_chain_P 1 > > > > > > > Protein_chain_L 1 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Protein_chain_H 1 > > > > > > > SOL 10 > > > > > > > SOL 127 > > > > > > > SOL 157 > > > > > > > SOL 41771 > > > > > > > CL- 8 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > Ahmet YILDIRIM > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Ahmet YILDIRIM > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > 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 > > > > > > > > > > > > > > > > > > > -- > > > Ahmet YILDIRIM > > > > > > > > > > > > > > > > > > > -- > > > > 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 > > > > > > > -- > Ahmet YILDIRIM > > >
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