[gmx-users] Segmentation fault

Hi When i perform mdrun for energy minimization, I found an error revealed segmentation fault. Please explain me -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] error in Solvation

of file 'GR.top' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University

[gmx-users] Re: topology error

only 59 particle variation found out of 230 ligand coordinates. On 8 October 2011 12:22, ITHAYARAJA ithayar...@gmail.com wrote: Dear Sir, I am actually simulating my protein with its ligand so I incorporated all ligand (3) coordinates to my protein .gro file and placed its .itp file also

[gmx-users] Ligand scattered out of the protein

. the ligand particles were scattered out of the pocket when I was doing configuration (editconf -bt triclinic -f trp1.pdb -o trp2.pdb -d 0.85). I was using GROMOS96 43a1 force field. Please help me to get out of this problem. -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar

[gmx-users] Re: gmx-users Digest, Vol 89, Issue 104

Dear Sir, when i am doing energy minimization (grompp), i found following error CMD : grompp -f em.mdp -c proteinGR_b4ion.gro -p proteinGR.top -o proteinGR_b4ion.tpr WARNING 1 [file em.mdp, line unknown]: Unknown or double left-hand 'coulomtype' in parameter file checking input for internal

[gmx-users] installation of FFTW

Hi I am working with RHEL 6 beta, I unable to install the FFTW package while installation I found the following error, make[3]: Leaving directory `/home/Ithayaraja/Desktop/ fftw-3.3.1-beta1/tools' make[2]: Leaving directory `/home/Ithayaraja/Desktop/fftw-3.3.1-beta1/tools' Making all in m4 make

[gmx-users] remove the atom clashes-reg

Is there any option to do the same. help me. Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype NR not found -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu

[gmx-users] Fatal error when position restraint the coordinates-reg

to -1, but normally it is better to fix the problem guide me to address this error... Thanks in advance... -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Error found on grompp - energy minimization

Dear sir, I struck with the following error when i perform energy minimization. I unable to understand what did it mean? please make me clear. So kindly do the needful. Fatal error: Atomtype CR1 not found -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University

[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97

but the following error also found, File input/output error: index.ndx I can do nothing by this simple statement, please help me, Sir Regards with, Ithayaraja M.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] Re: gmx-users Digest, Vol 86, Issue 97

Dear Sir, Above error was solved but the system has raised a following new error, i.e., Fatal error: 52 atoms are not part of any of the T-Coupling groups How do I find which atom file has problem? help me to solve this problem... -- ** Ithayaraja M, Research Scholar, Department

[gmx-users] Re: Dissociation of Ligand-reg

reference for your notice, likewise can we do simulation work? Dong Long, Yuguang Mu, Daiwen Yang Molecular Dynamics Simulation of Ligand Dissociation from Liver Fatty Acid Binding Protein Plos, 2009. On 13 June 2011 10:09, ITHAYARAJA ithayar...@gmail.com wrote: Dear Sir, Greeting! I

[gmx-users] Dissociation of Ligand-reg

regards with, -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

[gmx-users] Re: Fatal error: Atomtype CB not found

Thank you for your informative reply, Sir, Now I understood the problem but when i was tried with another ligand (GSSG) It could be simulated. Later I found error for different ligand. please give me the solution, what sort of force field should be applied? On 9 May 2011 21:27, ITHAYARAJA

[gmx-users] Fatal error: Atomtype CB not found

this problem. Thank you, Sir -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] error found in gmx

Hi Dear, I found a fatal error as I running pdb2gmx command, Which shows that incomplete ring in HIS341. I am very confused what it's meant and how do i solve the problem? Please any body give me a reasonable solution for that thank you -- -- *With love and gratitude of,* Ithayaraja M

[gmx-users] Re: gmx-users Digest, Vol 79, Issue 114

the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 79, Issue 114 ** -- -- *With love and gratitude of,* Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University

[gmx-users] Facing difficulty to install gromacs -reg

-- Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- 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