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? *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. 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. >> 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 <[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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