Hi, The .pdb file either should be dowloaded from RCSB website or you need to construct the structure by a software such as hyperchem and save the structure in .pdb format, so you are not supposed to get .pdb output through pdb2gmx command.
About the second problem, I think you need to chose the proper -ter. I've experienced these problem before and that was the problem. However I have not done the tutorial . Here others might help you better. In my person, OpenSuse and Ubuntu are proper options. Sincerely, Shima ________________________________ From: Hossein Lanjanian <[email protected]> To: [email protected] Sent: Friday, August 17, 2012 9:49 PM Subject: [gmx-users] 4 question 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 -- 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
