Hi we are new academic users of GROMACS. we installed gromacs 4.5.5 and tried to learn the job by using tutorials found in the "gromacs.org" web site. There is one question: we successfully ran the "1PGB.pdb". we know that *.pdb or *.gro files are necessary for the rest of analysis however we have not been able to get either of these two outputs from the first command " pdb2gmx -f 1PGB.pdb -ter ......" how is it possible??
Also we were trying to run membrane-receptor simulation, so we used gromacs.org tutorial again. according to that we got the "B2AR" protein but there were two problems with capping this protein: 1- when we ran the first command "pdb2gmx -f B2AR.pdb -o B2AR_processed.gro -ignh -ter " and chose the gromos96ff43a1" force-field and SPC water, the following error appeared: "there is a dangling bound at at least one of the terminal ends. select a proper terminal entry." when we omitted the "-ter" the error message changed to "there were 3 missing atoms in molecule protein_chain_A, if you want to use this incomplete topology anyhow, use the option -missing" after using "-missing" we encountered the following message "Residue 'MAL' not found in residue topology database" 2- there is no [ molecules ] section in the topology file, to modify as mentioned in the section two of tutorial. In the end: We have run GROMACS in different distributions of Linux such as Redhat, Centos and mint, nonetheless, which distribution do you recommend? your kind guidance is appreciated in advance. -- With The Best H.Lanjanian -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
