[gmx-users] Genion error
Hi, I have been trying to add ions to my system so as to make it neutral. However, I always obtain the same result: Solvent Group size (950) is not multiple of 9. The command I entered in this step was: genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+ -nname CL- How could I overcome this error? I realized this problem appears to be very common; however, I could not obtain an answer for my particular issue so far. Thanks in advance for your help. Best regards, *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia -- gmx-users mailing listgmx-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
Re: [gmx-users] Genion error
On 10/24/13 9:34 AM, felipe vasquez wrote: Hi, I have been trying to add ions to my system so as to make it neutral. However, I always obtain the same result: Solvent Group size (950) is not multiple of 9. What group did you choose at the genion prompt? The command I entered in this step was: genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+ -nname CL- Depending on your Gromacs version, this command may not be right. Ion names were changed as of version 4.5. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: [gmx-users] Genion error
Hi, I chose group 0 (System), but I also tried others like 1 (Protein) or 2 (Protein+H) with the same result. Regards, Andrés F. *Andrés Felipe Vásquez J., MSc.* Grupo de Fisiología Molecular Subdirección de Investigación Científica y Tecnológica Dirección de Investigación en Salud Pública Instituto Nacional de Salud Avenida calle 26 No. 51-20 - Zona 6 CAN Bogotá, D.C., Colombia 2013/10/24 Justin Lemkul jalem...@vt.edu On 10/24/13 9:34 AM, felipe vasquez wrote: Hi, I have been trying to add ions to my system so as to make it neutral. However, I always obtain the same result: Solvent Group size (950) is not multiple of 9. What group did you choose at the genion prompt? The command I entered in this step was: genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+ -nname CL- Depending on your Gromacs version, this command may not be right. Ion names were changed as of version 4.5. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] Genion error
On 10/24/13 10:21 AM, felipe vasquez wrote: Hi, I chose group 0 (System), but I also tried others like 1 (Protein) or 2 (Protein+H) with the same result. You don't want to embed ions into your protein or haphazardly into the system. You'll start deleting random segments of molecules, or the command will simply fail. You need to be replacing solvent molecules (usually water). Please consult some basic tutorial material; such selections are always covered. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
[gmx-users] genion error - No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’
Dear All, I need to add 6 CL ions to make the system neutral but when I type the command line genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6 and choose group 15 (SOL), the error is Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’ when I check the ‘topol.top’ file I found there are 24504 SOL molecules present. My topology file looks like this ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber99sb.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 Ligand 1 SOL 24504 Please let me know how to rectify the problem regards, Ashima -- View this message in context: http://gromacs.5086.n6.nabble.com/genion-error-No-line-with-moleculetype-SOL-found-the-molecules-section-of-file-topol-top-tp5005363.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
[gmx-users] genion error - No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’ [only with PROTEIN-LIGAND complex]
Dear All, I need to add 6 CL ions to make the system neutral but when I type the command line genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6 I am able to add the ion easily to a protein or protein-peptide complex by using the above command line where I replace the 6 SOL with 6 CL ions. But when I use the above command line for Protein-Ligand complex and choose group 15 (SOL), the error is Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’ when I check the ‘topol.top’ file I found there are 24504 SOL molecules present. My topology file looks like this ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber99sb.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 Ligand 1 SOL 24504 Please let me know how to rectify the problem regards, Ashima -- View this message in context: http://gromacs.5086.n6.nabble.com/genion-error-No-line-with-moleculetype-SOL-found-the-molecules-section-of-file-topol-top-only-with-P-tp5005368.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
[gmx-users] genion error { problem only with PROTEIN-LIGAND complex} - No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’
Dear All, I need to add 6 CL ions to make the system neutral but when I type the command line genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6 I am able to add the ion easily to a protein or protein-peptide complex by using the above command line where I replace the 6 SOL with 6 CL ions. But when I use the above command line for Protein-Ligand complex and choose group 15 (SOL), the error is Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’ when I check the ‘topol.top’ file I found there are 24504 SOL molecules present. My topology file looks like this ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber99sb.ff/ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols Protein_chain_A 1 Ligand 1 SOL 24504 Please let me know how to rectify the problem regards, Ashima -- View this message in context: http://gromacs.5086.n6.nabble.com/genion-error-problem-only-with-PROTEIN-LIGAND-complex-No-line-with-moleculetype-SOL-found-the-molecu-tp5005369.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
Re: [[gmx-users] genion error!]
Maybe you forgot to delete the waters that were removed in the ionization process? /Pär Dear users: I want to prepare protein simulation on 0.15mol/l salt concentration,I use genion command to add ions,After genion,I change cln.top file last line to NA+ 61,CL- 41. When I execute grompp ,there are warning : Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na) (more than 20 non-matching atom names) WARNING 1 [file cln.top, line 9059]: 102 non-matching atom names atom names from cln.top will be used atom names from cln_b4em.gro will be ignored I continue to execute mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr,There are some error: Fatal error: Too many LINCS warnings (10190) - aborting to avoid logfile runaway. This normally happens when your system is not sufficiently equilibrated,or if you are changing lambda too fast in free energy simulations. If you know what you are doing you can adjust the lincs warning threshold in your mdp file, but normally it is better to fix the problem. I don't know what happen ,could somebody tell me? Thank you very much! pdb2gmx -f 4cln.pdb -o cln.gro -p cln.top editconf -f cln.gro -o cln.gro -bt octahedron -c -d 0.75 genbox -cp cln.gro -cs spc216.gro -o cln_b4ion.gro -p cln.top grompp -f minim.mdp -c cln_b4ion.gro -p cln.top -o cln_b4ion.tpr genion -s cln_b4ion.tpr -o cln_b4em.gro -conc 0.15 -neutral grompp -f minim.mdp -c cln_b4em.gro -p cln.top -o cln_em.tpr mdrun -nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr grompp -f fullmd_sol.mdp -c minimized.gro -p cln.top -o fullmd.tpr mdrun -nice 0 -v -s fullmd.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php -- * Pär BjelkmarStockholm Center for Biomembrane Research Tel: +46-8-16 2746 Dep of Biochemistry and Biophysics Fax: +46-8-15 3679 Stockholm University [EMAIL PROTECTED] 10691 Stockholm, Sweden * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
[gmx-users] genion error!
Dear users: I want to prepare protein simulation on 0.15mol/l salt concentration,I use genion command to add ions,After genion,I change cln.top file last line to NA+ 61,CL- 41. When I execute grompp ,there are warning : Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na) (more than 20 non-matching atom names) WARNING 1 [file cln.top, line 9059]: 102 non-matching atom names atom names from cln.top will be used atom names from cln_b4em.gro will be ignored I continue to execute mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr,There are some error: Fatal error: Too many LINCS warnings (10190) - aborting to avoid logfile runaway. This normally happens when your system is not sufficiently equilibrated,or if you are changing lambda too fast in free energy simulations. If you know what you are doing you can adjust the lincs warning threshold in your mdp file, but normally it is better to fix the problem. I don't know what happen ,could somebody tell me? Thank you very much! pdb2gmx -f 4cln.pdb -o cln.gro -p cln.top editconf -f cln.gro -o cln.gro -bt octahedron -c -d 0.75 genbox -cp cln.gro -cs spc216.gro -o cln_b4ion.gro -p cln.top grompp -f minim.mdp -c cln_b4ion.gro -p cln.top -o cln_b4ion.tpr genion -s cln_b4ion.tpr -o cln_b4em.gro -conc 0.15 -neutral grompp -f minim.mdp -c cln_b4em.gro -p cln.top -o cln_em.tpr mdrun -nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr grompp -f fullmd_sol.mdp -c minimized.gro -p cln.top -o fullmd.tpr mdrun -nice 0 -v -s fullmd.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
Re: [gmx-users] genion error!
Qiang Zhong wrote: Dear users: I want to prepare protein simulation on 0.15mol/l salt concentration,I use genion command to add ions,After genion,I change cln.top file last line to NA+ 61,CL- 41. When I execute grompp ,there are warning : Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na) (more than 20 non-matching atom names) WARNING 1 [file cln.top, line 9059]: 102 non-matching atom names atom names from cln.top will be used atom names from cln_b4em.gro will be ignored I continue to execute mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr,There are some error: Hardly surprising... most gromacs warnings should be considered carefully. First the atom names in your .gro and .top files have to match those in the .atp files for the force field you're using. Then check the order and number of Na and Cl are correct. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
Re: [gmx-users] genion error!
On 2/28/2007 7:52 PM, Mark Abraham wrote: Qiang Zhong wrote: Dear users: I want to prepare protein simulation on 0.15mol/l salt concentration,I use genion command to add ions,After genion,I change cln.top file last line to NA+ 61,CL- 41. When I execute grompp ,there are warning : Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na) (more than 20 non-matching atom names) WARNING 1 [file cln.top, line 9059]: 102 non-matching atom names atom names from cln.top will be used atom names from cln_b4em.gro will be ignored I continue to execute mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e minim_ener.edr,There are some error: Hardly surprising... most gromacs warnings should be considered carefully. I think what Mark means is that in such case, you shall not continue to run mdrun without inspecting the warnings. First the atom names in your .gro and .top files have to match those in the .atp files for the force field you're using. Then check the order and number of Na and Cl are correct. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
