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 th

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 In

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

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

RE: [gmx-users] genion error!

Hi Zhong, It seems that you are not using the correct .top file. Once you finish adding ions with genion, you will need to generate a new topology, which also contains ions. Ciao, Luciano Dr. Luciano Triguero College of Art and Science Department of Chemistry Cox Science Building 1301 Memoria

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 : War

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 d

Re: [gmx-users] genion error!

Something seems wrong with your topology. It seems grompp gets confused about CL in one file being Na in the other. Maybe you added the last lines to cln.top in the wrong order. It doesn't necessarily cause the LINCS error later on, but suggests that your topology may need some more work.