[gmx-users] Which is better to make pqr files: pdb2pqr or GROMACS?

Hi all, I have a pdb file and I would like to make a pqr one. In GROMACS, I use editconf -mead to produce pqr, with topol.top taken from pdb2gmx or use it to produce pdb file, then use pdb2pqr. Which one is the better? Thank you so much. -- Gromacs Users mailing list * Please search the arc

Re: [gmx-users] Can't make links on GROMACS

So Google Groups doesn't allow you to import users, right? But I have seen Gromacs's Google Groups, however it has been abandoned since 2012, I don't know why. Also, I found another mail list which is better than the three ones I have mentioned above. It www.gmane.org. It also has statistic of each

Re: [gmx-users] Can't make links on GROMACS

Justin Lemkul writes: > > > On 5/13/14, 6:39 AM, Ly Minh Nhat wrote: > > Justin: why does it remove? > > At present, it doesn't really make sense. In 5.0-rc1, all the tools are simply > links to a binary called gmx that executes all of the programs, so linking to > links is really not con

Re: [gmx-users] Can't make links on GROMACS

I mean that it is a bug because you can't make link after build from the source, although it is easy to work around with it. -- 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.gr

Re: [gmx-users] Can't make links on GROMACS

Thanks, I work it out. My friend also meets this issue, is it really an issue? -- 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)sub

[gmx-users] Can't make links on GROMACS

have tried reinstall GROMACS with sudo make links but there is an error: ooker@ooker-Aspire-4741:~/gromacs-4.6.5/build$ sudo make links make: *** No rule to make target `links'. Stop. I have tried ln -s /usr/local/gromacs/bin/GMXRC /usr/local/bin/GMXRC or add alias gxmrc to ~./bashrc but

Re: [gmx-users] Error: illegal instruction (core dumped)

a GROMACS] < ml-node+s5086n5015337...@n6.nabble.com> wrote: > > > On 3/23/14, 11:57 AM, ooker wrote: > > sorry for spamming, but I need to up this thread. I'll delete this after > > someone answer. Sorry. > > > > You'll need to provide exact details of yo

Re: [gmx-users] Error: illegal instruction (core dumped)

sorry for spamming, but I need to up this thread. I'll delete this after someone answer. Sorry. -- View this message in context: http://gromacs.5086.x6.nabble.com/Error-illegal-instruction-core-dumped-tp5015293p5015331.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. --

Re: [gmx-users] Guidance on how to install Gromacs-5.0-beta2

Hi Pavan Kumar,Can you help me show the specific path to fftw? Thank you -- View this message in context: http://gromacs.5086.x6.nabble.com/Guidance-on-how-to-install-Gromacs-5-0-beta2-tp5014681p5015294.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users m