Thank you Shima for your kindly response On Aug 17, 2012 10:05 PM, "Shima Arasteh" <[email protected]> wrote:
> 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 > -- gmx-users mailing list [email protected] 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 list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
