Re: [gmx-users] g_membed failure

2016-10-17 Thread Tsjerk Wassenaar
;> 2016-09-14 13:47 GMT+03:00 Thomas Piggot <t.pig...@soton.ac.uk>: > >> > >>> > >> > >>> Hi, > >> > >>>> > >> > >>>> In more recent versions of GROMACS (4.6.x and above IIRC), the > >> > g_membed > &

Re: [gmx-users] g_membed failure

2016-10-17 Thread Sophia Kuriakidi
;> > >>>> command should either no longer work at all or print you a note to >> > tell >> > >>>> you >> > >>>> to use mdrun (depending upon version). >> > >>>> >> > >>>> My guess is that you

Re: [gmx-users] g_membed failure

2016-10-03 Thread Sophia Kuriakidi
might be what is causing the > > segmentation > > >>>> fault. That said, if I try a tpr from GROMACS 5.0.6 with g_membed > > 4.5.7 > > >>>> it > > >>>> does give me a warning about a mismatch of versions so I could be > > wron

Re: [gmx-users] g_membed failure

2016-10-02 Thread Mark Abraham
smatch of versions so I could be > wrong > >>>> (but what you say you are doing shouldn't be possible). > >>>> > >>>> Cheers > >>>> > >>>> Tom > >>>> > >>>> > >>>> On 14/09/16 08:40, Sotiri

Re: [gmx-users] g_membed failure

2016-10-02 Thread Sophia Kuriakidi
ssible). >>>> >>>> Cheers >>>> >>>> Tom >>>> >>>> >>>> On 14/09/16 08:40, Sotirios Dionysios I. Papadatos wrote: >>>> >>>> Hi, run some diagnostics, don't use the -xyinit etc >>>>> >

Re: [gmx-users] g_membed failure

2016-09-22 Thread Sophia Kuriakidi
nysios I. Papadatos wrote: >>> >>> Hi, run some diagnostics, don't use the -xyinit etc >>>> >>>> Try the basics gmx g_membed -f -p ... etc >>>> >>>> Also the way this worked for me was to use an index file. I made an >>>> index >>>> of the prot + lig + crys

Re: [gmx-users] g_membed failure

2016-09-21 Thread Thomas Piggot
mx-users-boun...@maillist.sys.kth.se < gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sophia Kuriakidi <skyriak...@gmail.com> Sent: Tuesday, September 13, 2016 9:18:12 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] g_membed failure Hi all, I am try

Re: [gmx-users] g_membed failure

2016-09-21 Thread Sophia Kuriakidi
.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sophia >> Kuriakidi <skyriak...@gmail.com> >> Sent: Tuesday, September 13, 2016 9:18:12 PM >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: [gmx-users] g_membed failure >> >> Hi all, >>

Re: [gmx-users] g_membed failure

2016-09-14 Thread Thomas Piggot
. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sophia Kuriakidi <skyriak...@gmail.com> Sent: Tuesday, September 13, 2016 9:18:12 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-use

Re: [gmx-users] g_membed failure

2016-09-14 Thread Sotirios Dionysios I. Papadatos
gmail.com> Sent: Tuesday, September 13, 2016 9:18:12 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] g_membed failure Hi all, I am trying to use g_membed in order to embed my protein in a lipid bilayer (I am using dppc). I am using the tutorial of Appendix A of this p

[gmx-users] g_membed failure

2016-09-13 Thread Sophia Kuriakidi
Hi all, I am trying to use g_membed in order to embed my protein in a lipid bilayer (I am using dppc). I am using the tutorial of Appendix A of this paper: *http://wwwuser.gwdg.de/~ggroenh/submitted/Membed_rev.pdf * I am creating an

[gmx-users] g_membed failure

2016-09-13 Thread Sophia Kuriakidi
Hi all, I am trying to use g_membed in order to embed my protein in a lipid bilayer (I am using dppc). I am using the tutorial of Appendix A of this paper: *http://wwwuser.gwdg.de/~ggroenh/submitted/Membed_rev.pdf * I am creating an