Re: [gmx-users] metal-oxide

jmaha...@polysci.umass.edu wrote: Hi, I want to create a metal-oxide lattice as one of the boundary of a cubic box containing protein and water. Does Gromacs supports interaction of metal ions with proteins and water? Actually what you need is a model physics (i.e. force field) that is known

[gmx-users] metal-oxide

Hi, I want to create a metal-oxide lattice as one of the boundary of a cubic box containing protein and water. Does Gromacs supports interaction of metal ions with proteins and water? Regards, JP -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-u

[gmx-users] How to put more solutes into the system ?

Hi The system = one protein molecule + 10 ligands + water molecules in 6 x 6 x 6 box. after 100 ns simulatin, 10 ligands have attached on the protein. Now, I tried to put another 10 ligands into the system. The steps are as follows. 1. Take one coordinate file and remove all the coordinates of th

[gmx-users] Segmentation Fault Problem

Hello, I am trying to determine the precise energies of a particular protein docking configuration. I have used the docking program FlexX to determine a potential binding mode. However, I am also trying to use AutoDock, and I am having a problem running AutoDockTools. Although the problem is no

Re: [gmx-users] How to put more solutes into the system ?

Chih-Ying Lin wrote: Hi The system = one protein molecule + 10 ligands + water molecules in 6 x 6 x 6 box. after 100 ns simulatin, 10 ligands have attached on the protein. Now, I tried to put another 10 ligands into the system. The steps are as follows. 1. Take one coordinate file and remove al

[gmx-users] Re: Help with Gromacs

Hi Pavan, Please, I'm not a user list. This is in no way attached to the tutorials of mine. But your problem arises because you're mixing things up. You're using a new run input (.tpr) file, and a checkpoint (.cpt) file. Either you continue runs using checkpoint files (preferred) or you generate

[gmx-users] Depth of penetration of DMPC lipid bilayer. How?

Be careful when you draw conclusions from your results though. I suggest that you start two simulations from different coordinates and look at their convergence. In my hands, this type of thing can take >> 1 us to converge, and that's without any major conformational changes in the peptide.

[gmx-users] make_edi fails with multiple eigenvectors for -linfix and -linacc

Hello, I am having trouble getting make_edi -linfix to work with multiple eigenvectors. This works for a single EV: $ echo 3 | make_edi -s ../../SETUP/makeTPR/edi.tpr -f ../../SETUP/makeEDI/eigenvec.trr -o testpositive.edi -linfix "1" -linstep "0.0001" -outfrq 50 And throws an error f

Re: [gmx-users] MSD

Quoting afsaneh maleki : > Hi, > > I am working on the simulation of protein memberane. > > How can I calculate MSD (mean squar displacement) of bond lipid ( as those > phosphate atomes are written 0.35 nm of protein)? > I know that I must use g_msd for calculating, but I need “index file” that >

Re: [gmx-users] Protein-ligand

Quoting "P.R.Anand Narayanan" : > Dear Gromacs users, > I am planning to bind a ligand to a protein and use gromacs to run the > simulations. But for using the pdb2gmx command, i heard we have to remove all > the ligands and cofactors associated with the protein. While pasting the > necessary part

Re: [gmx-users] Depth of penetration of DMPC lipid bilayer. How?

Quoting Kirill Bessonov : > Dear gromacs pros, > > I need to calculate depth of DMPC bilayer penetration by my 14 aa long > peptide. I'm not sure how to do it, but I have tried g_dist program and > calculated distance between DMPC and peptide groups for every frame of > simulation. Is that correct

RE: [gmx-users] g_mindist -or inconsistencies with atom-pairs

Thank you very much Ran, Will do. -Shay -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Ran Friedman Sent: Tuesday, December 22, 2009 16:53 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_mindist -or inconsistencie

Re: [gmx-users] Solvent Accessible Area with different Claculation Groups

Quoting Benjamin Lindner : > Hi, > > let me add some information here to clarify the problem we're facing: > > >>> I was wondering if anyone has some insight on why the two sasa values are > >>> not identical. > >>> > >>  From g_sas -h: > >> > >> "The calculation group should always consists of al

[gmx-users] Protein-ligand

Dear Gromacs users, I am planning to bind a ligand to a protein and use gromacs to run the simulations. But for using the pdb2gmx command, i heard we have to remove all the ligands and cofactors associated with the protein. While pasting the necessary parts of the ligand into the gro file, i hea

[gmx-users] Depth of penetration of DMPC lipid bilayer. How?

Dear gromacs pros, I need to calculate depth of DMPC bilayer penetration by my 14 aa long peptide. I'm not sure how to do it, but I have tried g_dist program and calculated distance between DMPC and peptide groups for every frame of simulation. Is that correct way of doing it or maybe there is a b

[gmx-users] How to put more solutes into the system ?

Hi The system = one protein molecule + 10 ligands + water molecules in 6 x 6 x 6 box. after 100 ns simulatin, 10 ligands have attached on the protein. Now, I tried to put another 10 ligands into the system. The steps are as follows. 1. Take one coordinate file and remove all the coordinates of th

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

Dear Mr Tsjerk Wassenaar : Thank you for your advice! I will try it! regards! --- 09年12月23日，周三, Tsjerk Wassenaar 写道： 发件人: Tsjerk Wassenaar 主题: Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection 收件人: "Discussion list for GROMACS users" 日期: 2009年1

Re: [gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?

Thank you, Mark, for your tip, the indexing solution is perfect! Regards, Vis --- On Tue, 12/22/09, Mark Abraham wrote: > From: Mark Abraham > Subject: Re: [gmx-users] trjconv -pbc: how to keep all parts of the system > "clustered" together in PDB? > To: "Discussion list for GROMACS users" >

[gmx-users] MSD

Hi, I am working on the simulation of protein memberane. How can I calculate MSD (mean squar displacement) of bond lipid ( as those phosphate atomes are written 0.35 nm of protein)? I know that I must use g_msd for calculating, but I need “index file” that is included phosphate atoms within 0.35

Re: [gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

Xi Zhao, I have no script either. It's not my homework, and I'm not on your payroll. If I need a script like that and write it, I'll be happy to share it with you. But that's not going to be soon. At present, I don't even have a data set to use to develop something like it. On the other hand, if y

Re: [gmx-users] (no subject)

Mohammad Ghahramanpour wrote: Hi all I want to insert two copies of my protein on the either side of the membrane. For insertion a single protein I used VMD and then the new desired protein coordination emerged in the membrane by using /genbox /command. But when I used the same procedure for

Re: [gmx-users] difference between rmsd and rmsf

what is difference between rmsd and rmsf? obviously, one has a "d" at the end while the other has a "f" ! google would tell you all about it! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

[gmx-users] difference between rmsd and rmsf

Hi what is difference between rmsd and rmsf? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interfa

[gmx-users] (no subject)

Hi all I want to insert two copies of my protein on the either side of the membrane. For insertion a single protein I used VMD and then the new desired protein coordination emerged in the membrane by using genbox command. But when I used the same procedure for two copies of the protein I have fa