Re: [gmx-users] doubts on g_confrms output

2011-02-12 Thread Tsjerk Wassenaar
gt; Mark >> >>> ------------------------ >>> *From:* Mark Abraham >>> *To:* Discussion list for GROMACS users >>> *Sent:* Saturday, February 12, 2011 0:01:39 >>> *Subject:* Re: [gmx-users] doubts on g_con

Re: [gmx-users] doubts on g_confrms output

2011-02-12 Thread David van der Spoel
ne is useful. Or you can chop apart the PDB by hand in a text editor. Mark *From:* Mark Abraham *To:* Discussion list for GROMACS users *Sent:* Saturday, February 12, 2011 0:01:39 *Subject:* Re: [gmx-users] doubts on g_confrms o

Re: [gmx-users] doubts on g_confrms output

2011-02-12 Thread Mark Abraham
On 12/02/2011 7:07 PM, Tsjerk Wassenaar wrote: Hi, The error message says the number of atoms in the first frame is not what was expected. That indicates the reference structure didn't match, which suggests the pdb file with the fitted structures wasn't used as reference. Solution: give the

Re: [gmx-users] doubts on g_confrms output

2011-02-12 Thread Tsjerk Wassenaar
Hi, The error message says the number of atoms in the first frame is not what was expected. That indicates the reference structure didn't match, which suggests the pdb file with the fitted structures wasn't used as reference. Solution: give the fitted structures both as reference (-s) and as traje

Re: [gmx-users] doubts on g_confrms output

2011-02-11 Thread Mark Abraham
hand in a text editor. Mark *From:* Mark Abraham *To:* Discussion list for GROMACS users *Sent:* Saturday, February 12, 2011 0:01:39 *Subject:* Re: [gmx-users] doubts on g_confrms output On 12/02/2011 2:55 AM, Kwee

Re: [gmx-users] doubts on g_confrms output

2011-02-11 Thread Kwee Hong
erk Wassenaar >To: Discussion list for GROMACS users >Sent: Saturday, January 22, 2011 15:53:22 >Subject: Re: [gmx-users] doubts on g_confrms output > > >Hi Joyce, >In pymol use 'set all_states' >Cheers, >Tsjerk >On Jan 22, 2011 8:30 AM, "Kwee Hong"

Re: [gmx-users] doubts on g_confrms output

2011-02-11 Thread Mark Abraham
Wassenaar *To:* Discussion list for GROMACS users *Sent:* Saturday, January 22, 2011 15:53:22 *Subject:* Re: [gmx-users] doubts on g_confrms output Hi Joyce, In pymol use 'set all_states' Cheers, Tsjerk On Jan 22, 2011 8:30 AM, "Kwee Hong" <mailto:jestan1...@yahoo.co

Re: [gmx-users] doubts on g_confrms output

2011-02-11 Thread Kwee Hong
Hi Tsjerk, Thanks for the help. I got it. But do you have any idea how to solve this in vmd? Regards, Joyce From: Tsjerk Wassenaar To: Discussion list for GROMACS users Sent: Saturday, January 22, 2011 15:53:22 Subject: Re: [gmx-users] doubts on g_confrms

Re: [gmx-users] doubts on g_confrms output

2011-01-21 Thread Tsjerk Wassenaar
Hi Joyce, In pymol use 'set all_states' Cheers, Tsjerk On Jan 22, 2011 8:30 AM, "Kwee Hong" wrote: Hi, I was trying to do some analysis following John's "GROMACS tutorial for solvation study of spider toxin peptide". I'm using GROMACS-4.5.3 and my command line for g_confrms is g_confrms -f1