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

[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 c

[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

[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

[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 fi

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!

Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938 -Original Message- From: [EMAIL PROTECTED] on behalf of Qiang Zhong Sent: Wed 2/28/2007 3:23 AM To: gmx-users@gromacs.org Subject: [gmx-users] genion error! Dear users: I want

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.

[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)