[gmx-users] input the gro and trr file into the VMD

Hi all users, When I try to input the .gro and .trr file into the VMD, I always find that there is no bond connected among the atoms.But in fact, I have defined all the bond connection in the gromacs files. Can anyone tell me how to get the snap shots in the VMD with the bonds among the atoms?

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Hi Mark, Thank you for your suggestion. As you know, I'm not familiar with the force field so i can't tell myself which one of the available force field is suitable to me. Fortunately, I find the force field Gromos96 and Amber have been adapted in previous studies. So guess i can use these kind

[gmx-users] (no subject)

Hi all users, When I try to input the .gro and .trr file into the VMD, I always find that there is no bond connected among the atoms.But in fact, I have defined all the bond connection in the gromacs files. Can anyone tell me how to get the snap shots in the VMD with the bonds among the atoms?

Re: [gmx-users] input the gro and trr file into the VMD

VMD defines the bonds according to a distance criteria. Note that these are not defined in a gro or trr file but in the tpr, which is not red by VMD. If your distances are not seen this means that the atoms are not within the VMD's criteria. Are you using a CG model where the distances are

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Hi, I'm not familiar with i can't tell myself which guess i can I have no idea whether This is the worst possible basis for trying to modify a force field. First get well acquainted with molecular dynamics and the role and whereabouts of force fields. Then you can start thinking of using

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Hi Tsjerk, Thanks a lot. Surely I can't modify the force field by my self. It's impossible to me to understand all of things you mentioned. So is it the only way to achieve my purpose? If so, it's so frustrating. I've been trying my best to contact with the author of one of my references. He

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Hi Ji, Well, if others have been there before, you can of course take from their experience. You haven't mentioned the substrate you're dealing with, though, so none of us can tell if we can offer the solution to your problem. First try to search the user list archives and the topology

[gmx-users] problem in gromacs installation

Hello All I have successfully installed gromacs by using source code gromacs-4.0.3 but when I run the GMXRC command the output is /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a function or sourced script /usr/local/gromacs/bin/GMXRC: line 44: CSH::

Re: [gmx-users] problem in gromacs installation

GMXRC is not to be ran but to sourced: source /path/GMXRC On Feb 19, 2009, at 12:35 PM, nitu sharma wrote: Hello All I have successfully installed gromacs by using source code gromacs-4.0.3 but when I run the GMXRC command the output is

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Hi Tsjerk, Sorry i did not supply any information about the enzyme/substrate system. Here, I'm studying the interaction between ester (substrate) and lipase (enzyme). The substrate contains C, O and H atoms. More details are shown in the following address.

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Ji Liu wrote: Hi Tsjerk, Sorry i did not supply any information about the enzyme/substrate system. Here, I'm studying the interaction between ester (substrate) and lipase (enzyme). The substrate contains C, O and H atoms. More details are shown in the following address.

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Hi, Even worse, this looks like a transition-state product. The hydrogen originating from the serine will not just have wandered off. It is unlikely that it happened to go sit on the other oxygen. Rather, the other oxygen, which would originally be double-bonded would probably form a strong

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Tsjerk Wassenaar wrote: Hi, Even worse, this looks like a transition-state product. The hydrogen originating from the serine will not just have wandered off. It is unlikely that it happened to go sit on the other oxygen. Rather, the other oxygen, which would originally be double-bonded would

[gmx-users] gromacs 4.0.4 kernel testing failure x86_64/linux

Hi, Thanks for the gromacs-4 test cases and the 4.0.4 release. :) CentOS-3 x86_64 gcc-3.2.3-59.x86_64 quote install procedure wget ftp://ftp.gromacs.org:/pub/gromacs/gromacs-4.0.4.tar.gz tar xzvf gromacs-4.0.4.tar.gz cd gromacs-4.0.4 ./configure --prefix=/../gromacs-4.0.4_fftw3_gnu --with-x

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Hi Ji, The big problem with transition states like these is that you can't properly describe the tetrahedral intermediate classically; you have to consider a whole bunch of non-classical interactions with the environment (the halfway transferred proton from serine to histidine, for instance).

[gmx-users] Virtual atom

Hello When a virtual atom is constructed from a two protein atoms, is it considered a protein atom itself? Should a residue called DUM be added to the aminoacids.dat file? Thanks. Best wishes George ___ gmx-users mailing list

Re: [gmx-users] problem in gromacs installation

On Thu, Feb 19, 2009 at 10:45 AM, nitu sharma sharmanit...@gmail.comwrote: *Dear All, I have compiled fft-3.2.1 in a specific user directory; then configured, compiled gromacs-4.0.3 from source code according to directions and installed it in the specific directory, all without any errors,

Re: [gmx-users] Virtual atom

Hi, The virtual atoms are residue-bound and will have the same residue name as the atoms it is constructed from. There's no residue name DUM introduced. Tsjerk On Thu, Feb 19, 2009 at 4:06 PM, Georgios Patargias g.n.patarg...@leeds.ac.uk wrote: Hello When a virtual atom is constructed from a

[gmx-users] replica restart from checkpoints

Dear Gromacs Users, I'm experiencing some problems when restarting a replica exchange run from previous checkpoint files. It often happens to me that the number of MD steps done in the previous run is not the same for all the replica. If this is the case, the program stops. This may happen

Re: [gmx-users] replica restart from checkpoints

Thanks for your reply... Which version are you using? In 4.0.3 I made things slightly better by allowing checkpoints to have different step numbers, as long as they fall within the same exchange attempt steps. I'm using 4.0.3. Same problem with the former versions 4.0.x. This could still

[gmx-users] input the gro and trr file into the VMD

Hi all users, When I try to input the .gro and .trr file into the VMD, I always find that there is no bond connected among the atoms.But in fact, I have defined all the bond connection in the gromacs files. Can anyone tell me how to get the snap shots in the VMD with the bonds among the atoms?

Re: [gmx-users] input the gro and trr file into the VMD

You've posted the same exact question five times today, even though you got a very good response already: http://www.gromacs.org/pipermail/gmx-users/2009-February/039830.html If you want free advice, take what you're given, demonstrate that you've made some efforts to solve your problem,

RE: [gmx-users] input the gro and trr file into the VMD

Hi, I am sorry for that cause every time I sent my question, it shows that this email was not delivered and hence, I just tried for many times. Yang From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul

[gmx-users] Ligand is moving far away after energy minimization

Dear Gromacs users, I am doing the MD of protein ligand complex. When I did the energy minimization of this complex, in the result , the ligand molceule is moving far away from the protein. What could be the possible reason? can anyone tell me how can i overcome this? Thanks in advance.

Re: [gmx-users] Ligand is moving far away after energy minimization

Ms. Aswathy S wrote: Dear Gromacs users, I am doing the MD of protein ligand complex. When I did the energy minimization of this complex, in the result , the ligand molceule is moving far away from the protein. What could be the possible reason? can anyone tell me how can i overcome