[gmx-users] simulation of a protein including calcium ion

Dear Justin thanks for your attention in my case calcium ion is bonded to 4 oxygen atoms of C=O group of protein. yes, Calcium ions are present in nearly all the force fields in Gromacs. but there are only parameters in * nb.itp and not in * bon.itp. how to obtain these new parameters for my

Re: [gmx-users] simulation of a protein including calcium ion

leila karami wrote: Dear Justin thanks for your attention in my case calcium ion is bonded to 4 oxygen atoms of C=O group of protein. yes, Calcium ions are present in nearly all the force fields in Gromacs. but there are only parameters in * nb.itp and not in * bon.itp. how to obtain

[gmx-users] simulation of a protein including calcium ion

Dear Justin Is there any way for this problem? -- 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

Re: [gmx-users] simulation of a protein including calcium ion

leila karami wrote: Dear Justin Is there any way for this problem? Please keep Tsjerk's comments (http://lists.gromacs.org/pipermail/gmx-users/2010-October/054938.html) in mind. If the calcium coordination complex plays only a minor structural role, you can probably justify using

[gmx-users] simulation of a protein including calcium ion

Hi gromacs users I want to study simulation of a protein including calcium ion. Can I use gromacs force fields? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] simulation of a protein including calcium ion

Hi I think it is a typical ligand in your pdb file.what do you think? if it be a ligand you can use PRODRG server to make topology file for your ligand and you must edit other files. please read this article: GROMACS Tutorial for Drug – Enzyme Complex best mohsen On Sat, Oct 16, 2010 at 11:32 AM,

[gmx-users] simulation of a protein including calcium ion

Dear mohsen ramezanpour* * yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but ERRDRG Too many atoms in this molecule (should be =300). PRODRG Program terminated unsuccessfully, sorry! -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] simulation of a protein including calcium ion

Dear Leila Ok,But you have to separate your ions from your general pdb file(protein+ions) in the form of pdb, in the other words you need to obtain the pdb files for your ions separately and then paste it to PRODRG server.because your protein has more than 300 atoms alonly. I hope it can help you

[gmx-users] simulation of a protein including calcium ion

Dear mohsen ramezanpour my pdb file has 3000atoms (protein) + 1 atom (calcium). Should I separate ion from general pdb again? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] simulation of a protein including calcium ion

Dear Leila Yes,I think so please read the article who I pointed,It can help you On Sat, Oct 16, 2010 at 12:16 PM, leila karami karami.lei...@gmail.comwrote: Dear mohsen ramezanpour my pdb file has 3000atoms (protein) + 1 atom (calcium). Should I separate ion from general pdb again?

Re: [gmx-users] simulation of a protein including calcium ion

leila karami wrote: Dear mohsen ramezanpour/ / yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but ERRDRG Too many atoms in this molecule (should be =300). PRODRG Program terminated unsuccessfully, sorry! There is no need to invoke PRODRG for

Re: [gmx-users] simulation of a protein including calcium ion

Hi, Do mind that calcium binding may involve (quantum) effects that are ill captured by classical force fields. If the binding site plays a central role in your research question, this may be problematic. Cheers, Tsjerk On Oct 16, 2010 2:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: leila