Dear Mark and Emanuel, I am sending the ions.tip and the topol.top files. Everything seems ok. Any problem about these files?
By the way, I am using the Gromacs 4.5.3. Force Field 43a1 25 Ocak 2011 12:03 tarihinde Emanuel Peter < emanuel.pe...@chemie.uni-regensburg.de> 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 * <ahmedo...@gmail.com> wrote: > > Dear Mark, > > I looked at gromacs mail list but I could not find a proper solution > .Whatshould > 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. > Seehttp://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 4177*1* > 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 4177*1* > CL- *8* > > > 25 Ocak 2011 10:49 tarihinde Mark Abraham <mark.abra...@anu.edu.au> yazdı: > >> >> >> On 01/25/11, *ahmet yıldırım * <ahmedo...@gmail.com> 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 gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Ahmet YILDIRIM > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
ions.itp
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topol.top
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