Re: [gmx-users] grompp error version 4.5.2

2010-11-22 Thread Adva Suez
my command was: /share/apps/gromacs-4.5.2/bin/grompp_mpi -f md.mdp -c ../../membed_17_npt.gro.884814.gro -t ../../membed_17_npt.trr.884814.trr -e ../../membed_17_npt.edr.884814.edr -p topol_protein_dppc_sol3_22.top -n index.ndx -o md_0_1_22.tpr the name of the edr file (and other NPT outputs) is

RE: [gmx-users] find the relevant structure out

2010-11-22 Thread #ZHAO LINA#
I really do not know how to get those beta-sheet structures out, or maybe by which ways? Any clues are warmly welcomed and appreciated. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Se

[gmx-users] Implementation of Andersen Thermostat

2010-11-22 Thread sapna sarupria
Dear All, I was just wondering if Andersen thermostat is implemented or going to be implemented in the recent/forthcoming versions of Gromacs. Is there anyone who has done it otherwise and would be willing to share an outline of the subroutines that they modified? Thanks in advance for your help

RE: [gmx-users] mdrun -rerun: bonded interactions of protein

2010-11-22 Thread NG HUI WEN
Thanks a lot for that Justin - I fully appreciate your point, thanks again! -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Tuesday, November 23, 2010 3:29 AM To: Discussion list for GROMACS users Subject: RE

Re: [gmx-users] protein folding

2010-11-22 Thread Lutz Maibaum
On Nov 22, 2010, at 3:09 AM, mohsen ramezanpour wrote: > I am searching for a tutorial for learning how to do protein folding with > Gromacs. > Do any one know such tutorials? Not exactly a tutorial, but you can find Gromacs input files, as well as several hundreds of microseconds worth of MD t

Re: [gmx-users] two problems with gromacs 4.5.3

2010-11-22 Thread Roland Schulz
On Mon, Nov 22, 2010 at 2:55 PM, Sanku M wrote: > Hi, > > When using gromacs 4.5.3, I experienced two problems ( neither of which > exist in gromacs 4.0.7 or older version like 3.3.3) > 1. when issuing grompp command to start one of my simulations, gromacs > 4.5.3 gives me fatal error: >

[gmx-users] two problems with gromacs 4.5.3

2010-11-22 Thread Sanku M
Hi, When using gromacs 4.5.3, I experienced two problems ( neither of which exist in gromacs 4.0.7 or older version like 3.3.3) 1. when issuing grompp command to start one of my simulations, gromacs 4.5.3 gives me fatal error: 'can not find atom type SNa .' However, with gromacs 4.0.

RE: [gmx-users] mdrun -rerun: bonded interactions of protein

2010-11-22 Thread Justin A. Lemkul
Quoting NG HUI WEN : > Dear Mark and Justin, > > > > I have a potentially silly question here. I have been trying to work out > the figures from the various options of g_energy. You mentioned before > that the bonded terms are not decomposable/require some hacking with the > .top file. I am a bit

Re: [gmx-users] How to obtain the coordinates of atom 100 with number in the frame 100 using xdrfile in C code

2010-11-22 Thread David van der Spoel
On 2010-11-22 13.36, wrote: Dear gmxers, I do not know whether this question is suitable here. If not, please just neglect it. However, this question puzzles me greatly, that is, how to obtain the coordinates of atom 100 with number in the frame 100 using xdrfile in C code. Here 100

Re: [gmx-users] protein folding

2010-11-22 Thread David van der Spoel
On 2010-11-22 13.27, Thomas Evangelidis wrote: With respect to protein folding, I want to fold a 42 amino acid loop (part of a protein domain with known structure) which has no homologous counterpart in PDB. Ab initio servers fail to assign a compact tertiary structure to the loop, so I would lik

[gmx-users] How to obtain the coordinates of atom 100 with number in the frame 100 using xdrfile in C code

2010-11-22 Thread 英雄不再寂寞
Dear gmxers, I do not know whether this question is suitable here. If not, please just neglect it. However, this question puzzles me greatly, that is, how to obtain the coordinates of atom 100 with number in the frame 100 using xdrfile in C code. Here 100 is only an example for some defined a

Re: [gmx-users] protein folding

2010-11-22 Thread Thomas Evangelidis
With respect to protein folding, I want to fold a 42 amino acid loop (part of a protein domain with known structure) which has no homologous counterpart in PDB. Ab initio servers fail to assign a compact tertiary structure to the loop, so I would like to see how MD tools can cope with this problem.

Re: [gmx-users] xtc corrupted during REMD

2010-11-22 Thread Mark Abraham
On 22/11/2010 7:11 PM, andrea spitaleri wrote: Hi, two on five have magic error at the same time. The simulation ends fine. Just the xtc files are corrupted. The magic error is systematic, since I repeated the simulation 4 times and I get the same behavior (at different time) after the continu

Re: [gmx-users] grompp error version 4.5.2

2010-11-22 Thread Mark Abraham
On 22/11/2010 11:03 PM, Adva Suez wrote: Hello, I'm using your KALP in DPPC tutorial to figure out how to simulate a molecule in a membrane in GROMACS. I'm using version 4.5.2 and from some reason I got an error in grompp whe trying generate md_0_1.tpr. the error is: Program grompp_mpi, VERS

[gmx-users] grompp error version 4.5.2

2010-11-22 Thread Adva Suez
Hello, I'm using your KALP in DPPC tutorial to figure out how to simulate a molecule in a membrane in GROMACS. I'm using version 4.5.2 and from some reason I got an error in grompp whe trying generate md_0_1.tpr. the error is: Program grompp_mpi, VERSION 4.5.2 Source code file: enxio.c, line: 1097

Re: [gmx-users] protein folding

2010-11-22 Thread ms
On 22/11/10 11:09, mohsen ramezanpour wrote: Dear All I am searching for a tutorial for learning how to do protein folding with Gromacs. Do any one know such tutorials? Please let me know them. I don't think so because managing to fold a protein in a MD simulation is no easy task. In theory,

Re: [gmx-users] protein folding

2010-11-22 Thread Mark Abraham
On 22/11/2010 10:09 PM, mohsen ramezanpour wrote: Dear All I am searching for a tutorial for learning how to do protein folding with Gromacs. Do any one know such tutorials? Please let me know them. There aren't any, because basically no proteins fold on the time scales that are accessible

Re: [gmx-users] .pqr to .pdb

2010-11-22 Thread Mark Abraham
On 22/11/2010 10:16 PM, mohsen ramezanpour wrote: Dear All I had a pdb file who was incomplete,there were not some atom coordinates in the file. I used a server who repaired it for me. The result was a .pqr file . Do you know any simple way for transforming .pqr file to .pdb? I want to s

[gmx-users] .pqr to .pdb

2010-11-22 Thread mohsen ramezanpour
Dear All I had a pdb file who was incomplete,there were not some atom coordinates in the file. I used a server who repaired it for me. The result was a .pqr file . Do you know any simple way for transforming .pqr file to .pdb? I want to see the structure with Pymol and it can't read pqr form

[gmx-users] protein folding

2010-11-22 Thread mohsen ramezanpour
Dear All I am searching for a tutorial for learning how to do protein folding with Gromacs. Do any one know such tutorials? Please let me know them. Thanks in advance Sincerely Mohsen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please s

RE: [gmx-users] mdrun -rerun: bonded interactions of protein

2010-11-22 Thread NG HUI WEN
Dear Mark and Justin, I have a potentially silly question here. I have been trying to work out the figures from the various options of g_energy. You mentioned before that the bonded terms are not decomposable/require some hacking with the .top file. I am a bit confused with that. As mention

RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

2010-11-22 Thread #ZHAO LINA#
When I went a bit further, I found it's wrong. Sorry. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Monday, November 22, 2010 4:50 PM To: Discussion list for GROMACS users Subject: RE: [g

RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

2010-11-22 Thread #ZHAO LINA#
I just tried the same way as using NA+, by genion -s ions.tpr -o protein_solvated_ions.gro -p topol.top -pname K+ -nname CL- -np Number_of_K It works, u may do a try. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Jignesh

Re: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

2010-11-22 Thread Erik Marklund
Jignesh Patel skrev 2010-11-22 08.57: Dear all, Can anybody tell me how to incorporate potassium ion parameters in GROMACS for GROMOS53a6 forcefield. Thanking you in anticipation. With regards, Jignesh If you have decent parameters, add them to ions.itp -- ---

Re: [gmx-users] xtc corrupted during REMD

2010-11-22 Thread andrea spitaleri
Hi, two on five have magic error at the same time. The simulation ends fine. Just the xtc files are corrupted. The magic error is systematic, since I repeated the simulation 4 times and I get the same behavior (at different time) after the continuing run. First time, I suspected for some I/O err