[gmx-users] bad bond in polymer

Hi gmx-users, I am building a polymer and I've added the monomer unit to the .rtp file. The final structure appears with an undesired bond between the monomer units at the extremes of the polymer. How can I prevent the monomers at the end forming the bond? I have read other post like http://w

Re: [gmx-users] bad bond in polymer

Hi, the bad bond appear in the topology (.top) file. veduardo. Lab. de Fisicoquímica Molecular Facultas de Ciencias Universidad de Chile From: nicegromacs Sent: Wednesday, August 12, 2009 8:28 PM To: gmx-users@gromacs.org Subject: [gmx-users] bad bond in polymer Hi gmx-users, I am

Re: [gmx-users] bad bond in polymer

CAJ CAI OAL OAK CAN CAM OAP OAO CAI CAH CAJ CAM -- From: "Justin A. Lemkul" Sent: Wednesday, August 12, 2009 9:23 PM To: "Discussion list for GROMACS users" Subject: Re: [gmx-users] bad bond in polymer nicegrom

Re: [gmx-users] bad bond in polymer

] C4F C5F CF9 -CAG -CAG -CAF -CAH C4F C1F CF9 O2F O3F C5F C4F O6F O7F CF9 CF8 C1F C4F -- From: "Justin A. Lemkul" Sent: Wednesday, August 12, 2009 9:50 PM To: "Gromacs Users' List" Subject: Re: [gmx-users] bad b

Re: [gmx-users] bad bond in polymer

roper --- "Stop Drinking My Beer !" (The Amps) nicegromacs wrote: CAG -CAM Defining a bond to a previous residue will certainly fail for at least one terminus of your polymer chain. You may find this post useful: http://oldwww.gromacs.org/pipermail/gmx-users/20

Re: [gmx-users] bad bond in polymer

-- From: "Justin A. Lemkul" Sent: Friday, August 14, 2009 12:14 PM To: "Gromacs Users' List" Subject: Re: [gmx-users] bad bond in polymer nicegromacs wrote: I follow some of the step of http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I omitt

Re: [gmx-users] bad bond in polymer

t;Gromacs Users' List" Subject: Re: [gmx-users] bad bond in polymer nicegromacs wrote: I follow some of the step of http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I omitted the change in the .hdb file because I don't have explicit hydrogens). Well, I bui

Re: [gmx-users] bad bond in polymer

. If things still aren't working out, please post: 1. The error message you are getting. 2. The .pdb file. 3. The current .rtp entries. -Justin nicegromacs wrote: Hi Justin, ups!! I am sorry this is the exact .pdb file. HETATM1 CAA DR0 1 83.043 46.127 36.820 1.00 0

[gmx-users] gyrate -p

Hi gmx-users, With respect to g_gyrate, Which is the algorithm difference between the default output and output with -p in g_gyrate? I have plotted both outputs one with -f -s -o and other with -f -s -o -p and the graphics are very different between both outputs Thank you in advance veduardo.

Re: [gmx-users] gyrate -p

Hi gmx-users, Well, with respect to -p option I understand what mean (principal component axes), but when -p is no placed in the command it is not clear, to me, how the program is working. Hi gmx-users, With respect to g_gyrate, Which is the algorithm difference between the default output a