Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...

2015-08-20 Thread Mark Abraham
Hi, Yes, see pdbgmx -h about merge. Probably you want -merge interactive -chainsep id Mark On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all, I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues.

Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded

2015-08-20 Thread Jorge Fernandez de Cossio Diaz
To: gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: fcd5150195922740996c04d9f8a6dfbb52c4c...@cimex2010mb1.cim.sld.cu Content-Type: text

Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...

2015-08-20 Thread Jorge Fernandez de Cossio Diaz
@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: CAMNuMARXoFeT_HN0J57y2pt=gzatnzgb+11asgpm6dxvyq3...@mail.gmail.com Content-Type: text/plain

Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ...

2015-08-20 Thread Justin Lemkul
, gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID: CAMNuMARXoFeT_HN0J57y2pt=gzatnzgb+11asgpm6dxvyq3...@mail.gmail.com

Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded

2015-08-20 Thread Justin Lemkul
From: Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu To: gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Broken protein chain: WARNING: Listed nonbonded interaction between particles ... Message-ID