Re: [gmx-users] CNT topology

sara wrote: Dear All Users I am beginner to GROMACS. I want to simulate CNT in water. I made pdb file by VMD and then made .gro by "editconf -f file.pdb -o file.gro -box 4" command. then for made topology file, I use .n2t itp, .itp, .rtp, ff.dat, and by "x2top -f file.gro -o topol.top -ff

Re: [gmx-users] CNT

On 20/01/2011 10:51 AM, trevor brown wrote: Hi Justin, I added lines to ffnonbonded.itp. It resulted in following error. It has some warnings and an error. I am interested in error. After that I will look at the warnings. In which file we may have an error? It is not specified. best wishes tr

RE: [gmx-users] CNT

The warning is due to having the molecules in the topology .top file listed in a different order to how they appear in the coordinate file, .gro The list within the topology has to be in the same order, even if you have broken up groups of the same molecules in the coordinate file. As for the

Re: [gmx-users] CNT

trevor brown wrote: Dear Justin, Regarding our previous discussion under "CNT" topic, you want to know exactly what I did to define C-C interaction. I have summarized it below. 1. I copied oplsaa.ff folder in my working directory 2. I added following lines to atomname2type.n2t Copls_995

Re: [gmx-users] CNT

trevor brown wrote: Dear friends, I have the following topology for system including CNT+peptide+water When I grompp for minimization, I got the following error. How can I solve it? best wishes trevor WARNING 1 [file ffbonded.itp, line 2703]: Overriding Bond parameters. old: 0.151 29

Re: [gmx-users] CNT

On 18/01/2011 10:25 AM, trevor brown wrote: Dear friends, I have constructed a .top file for a CNT by g_x2top. to do this I have added C-C interactions in .n2t file and also related ff in .atomtypes.atp. I have also a .top file for a peptide by pdb2gmx. My aim is to construct a simulation syste

Re: [gmx-users] CNT

trevor brown wrote: Dear users, In Gromacs 4.5.3, atom types are defined in /share/top/oplsaa.ff/atomtypes.atp. The corresponding bonds for diffrent atopm pairs are described as between opls_001 and opls_965. I have a CNT, I need C-C intereaction, which one should I choose? I would find a

Re: [gmx-users] CNT

On 01/05/11, mustafa bilsel wrote: > Hi all, > Could you tell me a program to obtain topol.top for a CNT? > In CNT.pdb residues are efined as UNK. > There may be some useful content here http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube Mark -- gmx-users mailing listgmx-users

Re: [gmx-users] CNT

mustafa bilsel wrote: Hi all, Could you tell me a program to obtain topol.top for a CNT? In CNT.pdb residues are efined as UNK. g_x2top is probably your best bet. Please have a thorough look through both the Gromacs site and the mailing list archive. Issues related to CNTs (especially the

Re: [gmx-users] CNT

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RE: [gmx-users] CNT

You must define residue name "UNK" in your topology file. Hero <[EMAIL PROTECTED]> schrieb: Hello, I plan to insert water molecules into a Single Wall NanoTube, I have generated the structure file of SWNT, but when I use: pdb2gmx -f SWNT_6_6_144.pdb -p SWNT.top -o SWNT.gro to form the

Re: [gmx-users] CNT

Quoting Hero <[EMAIL PROTECTED]>: > Hello, > > I plan to insert water molecules into a Single Wall NanoTube, > I have generated the structure file of SWNT, but when I use: > >pdb2gmx -f SWNT_6_6_144.pdb -p SWNT.top -o SWNT.gro > > to form the gro file, I got the following error: > >Fatal

Re: [gmx-users] CNT Simulation with GROMOS96 43a1 force field

Christopher Stiles wrote: I am simulating a carbon nanotube in water, I have been able to get it working for the Gromacs force field by modifying ffgmxbon.itp in the following way: # [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. ###

Re: [gmx-users] CNT Potassium doping with GROMACS

George Abadir wrote: Hi, I want to make a simulation of CNT in an environment of potassium atoms to see how they will be adsorbed on the CNT surface (this is a way of doping carbon nanotubes). I built a .pdb file with a CNT and some potassium atoms with random coordinates around the nanotu

Re: [gmx-users] CNT Potassium doping with GROMACS

Another point: is it possible to use pdb2gmx to do the job instead of x2top? I tried and used the GROMOS96 43b1 vacuum force field (since the doping by potassium is in vacuum), but i got the error"Residue 'CNT' not found in residue topolgy database'. I went to the 'ffg43b1.rtp' file in the /sha

Re: [gmx-users] CNT-protein interaction

Ok, thank you very much. Robert Johnson wrote: Just take the coordinate files for the protein and the nanotube, cat them together and then edit the resulting file. Then you can solvate the composite system using genbox. Bob On 5/10/07, George Abadir <[EMAIL PROTECTED]> wrote: Hi, I have

Re: [gmx-users] CNT-protein interaction

Just take the coordinate files for the protein and the nanotube, cat them together and then edit the resulting file. Then you can solvate the composite system using genbox. Bob On 5/10/07, George Abadir <[EMAIL PROTECTED]> wrote: Hi, I have built a topology file for a protein and a topolgy