Re: [gmx-users] .top file from .gro file

sunny mishra wrote: Hi Mark, I am sorry that I was not accurate in my scripts and I will not repeat this mistake again. Justin advised me that if the atoms are missing in .itp file and .gro file (Some of them are actually missing) then I have to model the atoms back in the ORIGINAL PDB file but

Re: [gmx-users] .top file from .gro file

Hi Mark, I am sorry that I was not accurate in my scripts and I will not repeat this mistake again. Justin advised me that if the atoms are missing in .itp file and .gro file (Some of them are actually missing) then I have to model the atoms back in the ORIGINAL PDB file but I din't quite get him.

Re: [gmx-users] .top file from .gro file

sunny mishra wrote: Hi Mark and Justin, Thanks for the valuable advise and I want to do the last test but before I proceed I just want to make sure If I am doing everything correct. Justin's advice was also very sound. If your model lacks relevant atoms, you have more work to do. Surely the MA

Re: [gmx-users] .top file from .gro file

As I said before, the original PDB file is missing atoms. You have to model them back in before you do anything else, otherwise MARTINI will expect them to be there and they won't be! -Justin sunny mishra wrote: Hi Justin and Mark, I just realized that I have some missing atoms in my .gro

Re: [gmx-users] .top file from .gro file

Hi Justin and Mark, I just realized that I have some missing atoms in my .gro file when I compared with .itp file and may be this is causing the problem. The atoms which are missing what should I do with them. Should I delete both from .itp and .gro file OR do i have to add in my .gro file and if I

Re: [gmx-users] .top file from .gro file

Alright. Sounds good to me. let me check that out and i will let you know the progress. Thanks, Sunny On Wed, Aug 19, 2009 at 7:19 PM, Justin A. Lemkul wrote: > > > sunny mishra wrote: > >> Hi Mark and Justin, >> >> Thanks for the valuable advise and I want to do the last test but before I >>

Re: [gmx-users] .top file from .gro file

sunny mishra wrote: Hi Mark and Justin, Thanks for the valuable advise and I want to do the last test but before I proceed I just want to make sure If I am doing everything correct. I got the 1K4C_cleanCG.seq file using grep command like this grep -A 1 1K4c_clean CG 1K4C_cleanCG.txt > 1K4C

Re: [gmx-users] .top file from .gro file

Hi Mark and Justin, Thanks for the valuable advise and I want to do the last test but before I proceed I just want to make sure If I am doing everything correct. I got the 1K4C_cleanCG.seq file using grep command like this grep -A 1 1K4c_clean CG 1K4C_cleanCG.txt > 1K4C_cleanCG.seq Now my next s

Re: [gmx-users] .top file from .gro file

In addition to everything Mark said, also realize that there may be a fundamental problem in everything you are doing: there are missing atoms in the original 1K4C structure. If you have not modeled them back in, the appropriate CG particles will not necessarily all be placed in your CG struc

Re: [gmx-users] .top file from .gro file

sunny mishra wrote: Hi Justin, Thanks for the reply and here is the following which I am doing. I would appreciate if you can point out my errors. 1) I am working on 1K4C (KcSA) and i downloaded that from www.pdb.org and after that I cleaned the PBD file, removed all the HETATOMS and ATOMS wit

Re: [gmx-users] .top file from .gro file

Hi Justin, Thanks for the reply and here is the following which I am doing. I would appreciate if you can point out my errors. 1) I am working on 1K4C (KcSA) and i downloaded that from www.pdb.org and after that I cleaned the PBD file, removed all the HETATOMS and ATOMS with ligand A & B and als

Re: [gmx-users] .top file from .gro file

sunny mishra wrote: Hi, I checked both the files they match exactly but still I get the same error message that .gro file and .top file dnt match. I dnt know how to proceed now. Well, something has to be wrong, or else grompp wouldn't complain. You say you've checked the .top, but have

Re: [gmx-users] pbc = xyz with mdrun -pd ?

Chih-Ying Lin wrote: Hi I am setting pbc = xyz ; and type the commands grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated => the simulation failed and .out file suggested me to use the flag -pd. grompp

Re: [gmx-users] .top file from .gro file

Hi, I checked both the files they match exactly but still I get the same error message that .gro file and .top file dnt match. I dnt know how to proceed now. Sunny On Tue, Aug 18, 2009 at 8:18 PM, sunny mishra wrote: > Ok..I will see that and let you know. Thanks for the help though. > Sunny > >

[gmx-users] pbc = xyz with mdrun -pd ?

Hi I am setting pbc = xyz ; and type the commands grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated => the simulation failed and .out file suggested me to use the flag -pd. grompp_mpi -v -f minim.mdp -c 6LYZ-

Re: [gmx-users] For free energy landscape!

dxli75 wrote: Dear All, I have make a free energy landscape by using the data of RMSD and H-bond number of main chain of a protein according to the following method. I am not sure if the method does work. If not, Could you give me some advises? Thank you! PS: Method 1. Obtained t

[gmx-users] For free energy landscape!

Dear All, I have make a free energy landscape by using the data of RMSD and H-bond number of main chain of a protein according to the following method. I am not sure if the method does work. If not, Could you give me some advises? Thank you! PS: Method 1. Obtained the RMSD and the nu

Re: [gmx-users] cluster graph

Hey, According to the urban dictionary: II. Defining 'Noob' Contrary to the belief of many, a noob/n00b and a newbie/newb are not the same thing. Newbs are those who are new to some task* and are very beginner at it, possibly a little overconfident about it, but they are willing to learn and fix

[gmx-users] pulling

Hey, has anyone actually succeeded doing pulling with gromacs 4.0.5 keeping the distance between a froozen and a non froozen group (so not pulling into a direction but just applying the harmonic potential to the distance). If so, could you send me the mdp file showing how you set up the whole thin

[gmx-users] cluster graph

Dear all, I am difficulty to understand the lable of the cluster size, what is the y-axis (labelled #structure) and x-axis (labelled as cluster#). what does the lable means? I used this command g_cluster -f md.xtc -s md.tpr -method gromos -o cluster.xvg thanks for comments... T