Fatemeh, Best to keep this to the emailing list. Then others can find it later that have a similar issue, or others can provide information.
>I want to investigate the adsorption of H2 and also CO on MOFs (metal organic frameworks), in .top file I >introduce CO and the number of it that is 1, but it gives error( no such molecule type CO), as you told I >went to atomtype.atp file to find atom type for C and H but as I saw, the atomtype for carbonyle oxygen >is O and for bare carbon is C, and the others are not related, when I introduce CO in this way it gives >error, when I introduce it one by one, C separately and O separately also it gives error that no such >atomtype C or O, I do not know how should I introduce CO? could you help me with my problem? What it sounds like you are missing is the topology file that provides information on how the molecules are constructed, what is what the first error you obtained is telling you. You have to provide information to the program on how the molecule is put together, bonds, forces etc. That is either done within the .top file, or via a separate .itp file that is subsequently included within the .top file. http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#molecule-itp-file I would highly recommend that you step back for a moment and do some tutorials using GROMACS. They won't be with the system you are going to perform the calculations on, but you need to develop a fundamental understanding of how these simulations work, what information you need to provide to them, why etc. Otherwise you are going to waste a lot of time, and more than likely generate something that cannot be used. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 25 Feb 2019 at 08:34, Dallas Warren <dallas.war...@monash.edu> wrote: > The molecule name you have in your .top file, in the [ molecules ] > section, does not match the molecule name in your .itp (could also be > within your .top) file, in the [ moleculetype ] section. > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On Mon, 25 Feb 2019 at 02:24, banijamali_fs <banijamali...@ut.ac.ir> > wrote: > >> Hi there, >> >> I'm simulating the adsorption of H2 on a structure (Metal organic frame >> work), after making the pdb structure and running the first cmmand of >> gromacs to have gro file, I added two atoms of CU and one hydrogen >> molecule to the gro file and also changed the number of the atoms at the >> top of gro file. Then I run the following commands up to the command >> about energy minimization that I got this error( No such molecule type >> hydrogen), I want to ask that, gromacs knows H2 molecule, why it says >> that, no such molecule type? it means that I should introduce it agin in >> aminoacids.rtp file? >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
