Re: [gmx-users] Error in Analysis Script RMSD

Arneh Babakhani wrote: Hi, I'm experiencing an awkward error. I created an analysis script to calculate some RMSDs (I've pasted the script below). When I try to run the script, I get an error. The following is the output. Option Filename Type Description

Re: [gmx-users] Error in Analysis Script RMSD

Arneh Babakhani wrote: Hi, I'm experiencing an awkward error. I created an analysis script to calculate some RMSDs (I've pasted the script below). When I try to run the script, I get an error. The following is the output. Option Filename Type Description

Re: [gmx-users] Error in Analysis Script RMSD

On 5/23/07, David van der Spoel [EMAIL PROTECTED] wrote: Arneh Babakhani wrote: Hi, I'm experiencing an awkward error. I created an analysis script to calculate some RMSDs (I've pasted the script below). When I try to run the script, I get an error. The following is the output. Option

[gmx-users] how to avoid pdb2gmx from deleting duplicates?

Hi there, Thanks for the last reply, sorry i made a mistakes when writing previous mail. I ran several tests, that's why the output is micelle_3.top and not micelle_1 like i state in the command. If my pdb2gmx command was right (regardless what file name for .gro and .top i put ) , and the

Re: [gmx-users] how to avoid pdb2gmx from deleting duplicates?

Alif M Latif wrote: Hi there, Thanks for the last reply, sorry i made a mistakes when writing previous mail. I ran several tests, that's why the output is micelle_3.top and not micelle_1 like i state in the command. If my pdb2gmx command was right (regardless what file name for .gro and

[gmx-users] how to find out the average running structure

Hi everybody, i am a new user of gromacs, i had run simulation for 10,0 iterations with the protein 1f9b and have obtained all the required output files. after comparing and analysing the potential energy.xvg file and rms(root mean square deviation).xvg file i have found out that there is

Re: [gmx-users] Range checking error issue

Matteo Guglielmi wrote: Hello world, the following is my input file: title= 2masn cpp = /usr/bin/cpp define = -DPOSRES integrator = md tinit= 0 dt = 0.002 nsteps

Re: [gmx-users] how to find out the average running structure

Sonali wrote: Hi everybody, i am a new user of gromacs, i had run simulation for 10,0 iterations with the protein 1f9b and have obtained all the required output files. after comparing and analysing the potential energy.xvg file and rms(root mean square deviation).xvg file i have found out

Re: [gmx-users] how to find out the average running structure

Hi, On Wednesday, 23. May 2007 10:04, Sonali wrote: Hi everybody, i am a new user of gromacs, i had run simulation for 10,0 iterations with the protein 1f9b and have obtained all the required output files. after comparing and analysing the potential energy.xvg file and rms(root mean

[gmx-users] Re: readxtc can not get coordinates without jump?

Hi, Tsjerk I see, you are right. I checked the coordinates again. Readxtc can give correct coordinates without jumps. And it seems that we should be careful when using trjconv to extract coordinates without jumps. Zhongqiao

[gmx-users] fatal error

hi everybody, i am a new user of gromacs,while trying to run with the tool g_covar for finding out an average running structure i am getting the following error. Program g_covar, VERSION 3.3 Source code file: smalloc.c, line: 113 Fatal error: calloc for mat (nelem=997170084, elsize=4, file

Re: [gmx-users] g_dist problems

Edvin Erdtman wrote: Which compiler did you use? This maybe says more: $ file /usr/bin/g_dist /usr/bin/g_dist: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), stripped I copied the file to another machine. And there

[gmx-users] Restarting AFM pulling

Hello everyone, I'me trying to run a very long simulation with the AFM pulling, which should be partitioned into many smaller pieces. However, this seems that the pull code does not preserve the force even if the position of the spring is set to what was observed at the end of the previous run.

[gmx-users] do_dssp for many peptides

Dear all, I have a problem with applying do_dssp to a system containing 24 peptides with 15 residues and 124 atoms per peptide (solvent removed, deshuffled). I observe the following behavior: (1) When I try to apply dssp to all peptides, do_dssp says There are 1668 residues in your

[gmx-users] atom type not found error

Hello everybody; when I try to create the .tpr file from my .gro and .top files, using command grompp, there is an error saying atomtype (e.g. OS) not found. when I look at the .atp file at gromacs directory,the atom types and their corresponding masses exist there.what could be the problem and

RE: [gmx-users] problem with freeze-group : Large VCM(Berk Hess)

From: jagannath mondal [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: RE: [gmx-users] problem with freeze-group : Large VCM(Berk Hess) Date: Sat, 12 May 2007 19:18:46 +0100 (BST) Hi

Re: [gmx-users] fatal error

Am Mittwoch, 23. Mai 2007 schrieb Sonali: Program g_covar, VERSION 3.3 Source code file: smalloc.c, line: 113 Fatal error: calloc for mat (nelem=997170084, elsize=4, file gmx_covar.c, line 219) --- Whatever Happened to Pong ? (F. Black)

Re: [gmx-users] fatal error

From: Martin Höfling [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] fatal error Date: Wed, 23 May 2007 13:20:42 +0200 Am Mittwoch, 23. Mai 2007 schrieb Sonali: Program

[gmx-users] pdb2gmx -merge option take a *very* long time, and doesn't work ...

time pdb2gmx -v -f 1HPV.pdb -o 1HPV_gro.pdb -p 1HPV_gro.top -i 1HPV_posre.itp -ff G53a6 -posrefc 100 -ignh -merge pdb2gmx1.log ... more than 15 minutes (and counting ...) while it is instataneous without the merge option. (my computer is a dual ahtlon 3800+, not that slow ...). As i

[gmx-users] bootstrap problem

Thanks you all for your replies. I have downgraded automake to 1.9.6 version and bootstrap script works fine now. Best regards, Tom ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] atom type not found error

Hard to tell from that amount of information... Seems, you don't include a forcefield... Please describe in more detail, what you exactly did and maybe post the head of your topology-file... Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical

Re: [gmx-users] bootstrap problem

Test... __ Od: [EMAIL PROTECTED] Komu: gmx-users gmx-users@gromacs.org Datum: 23.05.2007 13:44 Předmět: [gmx-users] bootstrap problem Thanks you all for your replies. I have downgraded automake to 1.9.6 version and bootstrap

Re: [gmx-users] do_dssp for many peptides

Volker Knecht wrote: Dear all, Does anyone have an idea what is going wrong? No, but it would straightforward to write a script that used trjconv while iterating through a set of index files that extract the coordinates of just one peptide at a time, write that to an intermediate .xtc

[gmx-users] make gmx_disre.c error

Dear gromacs users, i would like to compile 3-3 gromacs revision (cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r release-3-3-patches gmx). Configure script ended with no apperantly problems but make ended with this error: gmx_disre.c: In function 'gmx_disre': gmx_disre.c:601:

RE: [gmx-users] make gmx_disre.c error

From: [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users gmx-users@gromacs.org Subject: [gmx-users] make gmx_disre.c error Date: Wed, 23 May 2007 14:57:07 +0200 Dear gromacs users, i would like to compile 3-3 gromacs revision (cvs -z3 -d

[gmx-users] (no subject)

Dear sir: I'm a newcomer to gromacs,and I'm reading the manual for *.top file. I can't not understand the keyword EXLUSION. What does it mean? It prefers to the bond between two particles or no bond between them, I am confused a little. Thanks a lot! Regards, Zhang

Re: [gmx-users] (no subject)

ZhouLong Zhang wrote: Dear sir: I'm a newcomer to gromacs,and I'm reading the manual for *.top file. I can't not understand the keyword EXLUSION. What does it mean? It prefers to the bond between two particles or no bond between them, I am confused a little. See manual sections 4.6.1 and

[gmx-users] Re: Re: do_dssp for many peptides

Dear all, Does anyone have an idea what is going wrong? No, but it would straightforward to write a script that used trjconv while iterating through a set of index files that extract the coordinates of just one peptide at a time, write that to an intermediate .xtc file and send that

RE: [gmx-users] FEP with real or dummy charges?

Thanks again for the reply. A virtual point charge is what I want. Best wishes George -Original Message- From: [EMAIL PROTECTED] on behalf of Maik Goette Sent: Wed 5/23/2007 12:51 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] FEP with real or dummy charges? No.

Re: [gmx-users] Re: Re: do_dssp for many peptides

do_dssp claims that are 248 residues in my selected group, although 248 is the number of *atoms* (not of residues) of this peptide. After the notion that some temporary file is backed up, do_dssp gets stuck again. I have even tried exactly Mark's suggestion (xtc file containing single

Re: [gmx-users] Error in Analysis Script RMSD

Ahh yes, you're right. The script is in the right directory, but for some reason it keeps reverting back to my home directory. I threw in a cd line to fix it. Thanks for the help! Arneh Mark Abraham wrote: Arneh Babakhani wrote: Hi, I'm experiencing an awkward error. I created an

[gmx-users] do_dssp: main chain

Dear all, Message: 4 Date: Wed, 23 May 2007 10:16:59 -0400 From: Justin Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: Re: do_dssp for many peptides To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1

[gmx-users] g_angle dihedrals

When I run a simulation (md) with hydrogen peroxide, and then view the resulting structure in vmd I get a dihedral angle through all the atoms (sequentially H-O-O-H) I get a value of 4.92, I also got the same value using ghemical. However, when I run g_angle I can't seem to match that value.

Re: [gmx-users] do_dssp: main chain

Hi, perhaps your .trr has some errors. Have you tried converting it or gmxcheck? Other solution could be: Transfer your protein residues to an multiple pdb file and try do_dssp again. Perhaps your top or ndx doesn't fit. On Wednesday, 23. May 2007 17:07, Volker Knecht wrote: Dear all,

[gmx-users] Stuck ...

Mark Abraham a écrit : Stéphane Téletchéa wrote: While switching from NVT to NPT, i'm crashing my simulation. The error message seen is (repeated 10 times, then mdrun aborts): # Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20 -1.59647e+20 -1.59647e+20 Correcting invalid

[gmx-users] hacked...

It seems the GROMACS web site has been hacked and perhaps loaded with unpleasant things. May be advisable to stay away until the GROMACS gurus let us know the coast is clear. David ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] hacked...

Hi David, Thanks - I already noticed and just put the old site online instead, so hopefully it should be safe to visit for now. We'll see if we can move to something safer/more stable than Joomla. I'm sure there might have been some security update, but it's getting tedious to keep up

Re: [gmx-users] pdb2gmx -merge option take a *very* long time, and doesn't work ...

Stephane, As an exercise, try running pdb2gmx without redirection of the output... Try to understand the programs and the options before trying to script things (including redirecting input/output). Tsjerk On 5/23/07, Stéphane Téletchéa [EMAIL PROTECTED] wrote: time pdb2gmx -v -f 1HPV.pdb -o

Re: [gmx-users] how to find out the average running structure

Hi Sonali, g_rmsf also gives average structures if you request so. It avoids the covariance matrix construction/diagonalization g_covar does and will save some time :) Tsjerk On 5/23/07, Florian Haberl [EMAIL PROTECTED] wrote: Hi, On Wednesday, 23. May 2007 10:04, Sonali wrote: Hi

Re: [gmx-users] Constraining N-H and H-H bonds in ammonium via SETTLE?

Hi John, On May 23, 2007, at 9:09 PM, John D. Chodera wrote: Hi all, Can the SETTLE implementation in gromacs be used to constrain N-H and H-H bond lengths in ammonium (NH4+) molecules? We have prepared an .itp file (attached below) -- based on the Pande group ffamber port -- for

Re: [gmx-users] Stuck ...

Stéphane Téletchéa wrote: Mark Abraham a écrit : Stéphane Téletchéa wrote: While switching from NVT to NPT, i'm crashing my simulation. The error message seen is (repeated 10 times, then mdrun aborts): # Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20 -1.59647e+20

Re: [gmx-users] Stuck ...

Hi Stephane, I think this ends up in treating symptoms. Setting up a simulation of HIVP should not give such problems. It's probably best to start all over: pdb2gmx, EM in vacuum, editconf -d 1.0, genbox, EM in solvent, etc... Keep track of everything you're doing, give all files an informative