Re: [gmx-users] Re: eigenvectors in readable format

Hi Rama, You can convert the .trr file to readable .gro/.g96 with trjconv. Frames with positive times will correspond to eigenvectors; the time indicates the eigenvector index. Make sure not to use any options like pbc/fitting :p Cheers, Tsjerk On Sat, Oct 16, 2010 at 7:00 AM, Ramachandran G

Re: [gmx-users] Re: eigenvectors in readable format

Hi Tsjerk, Thank you very much for your help. Cheers! Rama On Fri, Oct 15, 2010 at 11:00 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Rama, You can convert the .trr file to readable .gro/.g96 with trjconv. Frames with positive times will correspond to eigenvectors; the time

[gmx-users] simulation of a protein including calcium ion

Hi gromacs users I want to study simulation of a protein including calcium ion. Can I use gromacs force fields? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] PRODRG server

Dear gromacs users I have a pdb file who include protein and a drug.I separated them by pymol software and saved them separately.now I want to make topology and gro file for it but I am facing with this page below.can you guid me? thanks in advance. PRODRG Starting up PRODRG version 071121.0636

Re: [gmx-users] simulation of a protein including calcium ion

Hi I think it is a typical ligand in your pdb file.what do you think? if it be a ligand you can use PRODRG server to make topology file for your ligand and you must edit other files. please read this article: GROMACS Tutorial for Drug – Enzyme Complex best mohsen On Sat, Oct 16, 2010 at 11:32 AM,

[gmx-users] Re: PRODRG server

actually the final massage was :Unfortunately PRODRG crashed On Sat, Oct 16, 2010 at 11:36 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Dear gromacs users I have a pdb file who include protein and a drug.I separated them by pymol software and saved them separately.now I want

[gmx-users] simulation of a protein including calcium ion

Dear mohsen ramezanpour* * yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but ERRDRG Too many atoms in this molecule (should be =300). PRODRG Program terminated unsuccessfully, sorry! -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] simulation of a protein including calcium ion

Dear Leila Ok,But you have to separate your ions from your general pdb file(protein+ions) in the form of pdb, in the other words you need to obtain the pdb files for your ions separately and then paste it to PRODRG server.because your protein has more than 300 atoms alonly. I hope it can help you

[gmx-users] simulation of a protein including calcium ion

Dear mohsen ramezanpour my pdb file has 3000atoms (protein) + 1 atom (calcium). Should I separate ion from general pdb again? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] simulation of a protein including calcium ion

Dear Leila Yes,I think so please read the article who I pointed,It can help you On Sat, Oct 16, 2010 at 12:16 PM, leila karami karami.lei...@gmail.comwrote: Dear mohsen ramezanpour my pdb file has 3000atoms (protein) + 1 atom (calcium). Should I separate ion from general pdb again?

[gmx-users] pdb2gmx stop at AtomType 1

Dear gmx-users, I have added the required residue groups in the rtp file. Then I run the pdb2gmx using the following line for the top file, only to stop at AtomType 1. No any message is given. I can not think out what is happening at all. Please help me with this problem, thanks a lot. Note

Re: [gmx-users] simulation of a protein including calcium ion

leila karami wrote: Dear mohsen ramezanpour/ / yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but ERRDRG Too many atoms in this molecule (should be =300). PRODRG Program terminated unsuccessfully, sorry! There is no need to invoke PRODRG for

Re: [gmx-users] Re: PRODRG server

These error messages are likely more important: PRODRG WARNING: multiplicity of generated molecule is not 1. PRODRG WARNING: bond type assignment failed at C13 There is something about the chemical structure involving this atom that PRODRG can't handle. Based on the information you've

Re: [gmx-users] pdb2gmx stop at AtomType 1

wrote: Dear gmx-users, I have added the required residue groups in the rtp file. Then I run the pdb2gmx using the following line for the top file, only to stop at AtomType 1. No any message is given. I can not think out what is happening at all. Please help me with this

[gmx-users] User training for Gromacs on parallel systems: a survey

Dear all, Gromacs is participating in the ScalaLife (http://scalalife.org/) European project aimed at improving the parallel performance of Life Science applications. An important part of the ScalaLife project is the dissemination of the results and user training. We have prepared a short

Re: [gmx-users] Re: PRODRG server

Dear justin no,I had not done it. But this two warning are not present in other my molecules,for example I tested another molecule but the massage was: defaults to zero instead of generating an error PRODRG PRODRG PRODRG Starting up PRODRG version 071121.0636 PRODRG

Re: [gmx-users] Re: PRODRG server

mohsen ramezanpour wrote: Dear justin no,I had not done it. But this two warning are not present in other my molecules,for example I tested another molecule but the massage was: defaults to zero instead of generating an error PRODRG PRODRG PRODRG Starting up

Re: [gmx-users] simulation of a protein including calcium ion

Hi, Do mind that calcium binding may involve (quantum) effects that are ill captured by classical force fields. If the binding site plays a central role in your research question, this may be problematic. Cheers, Tsjerk On Oct 16, 2010 2:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: leila

[gmx-users] position restraints and out of bounds atom index

Hi all I'm trying to simulate a system with 3 chains (A, H and L). Pb2gmx gave me 3 .itp files (one for each chain), each one with atom number starting from 1, and a .top file with these 3 .itp included. It gave me also a .gro file with the 3 chains numbered consecutively (the atom number

[gmx-users] g_dipole ? = dipole moment ?

Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time?

Re: [gmx-users] g_dipole ? = dipole moment ?

On 2010-10-16 21.36, Chih-Ying Lin wrote: Hi I issue the g_dipole command on Gromacs = And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for

Re:[gmx-users] pdb2gmx stop at AtomType 1(Justin)

Date: Sat, 16 Oct 2010 08:36:00 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb2gmx stop at AtomType 1 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4cb99c30.50...@vt.edu Content-Type: text/plain; charset=x-gbk; format=flowed 英雄不再寂寞 wrote: Dear

Re: [gmx-users] pdb2gmx stop at AtomType 1(Justin)

英雄不再寂寞 wrote: Date: Sat, 16 Oct 2010 08:36:00 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] pdb2gmx stop at AtomType 1 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4cb99c30.50...@vt.edu Content-Type: text/plain; charset=x-gbk; format=flowed