[gmx-users] IMAC enable GPU problem

/clang++ AppleClang 9.0.0.939 C++ compiler flags: -msse4.1-std=c++11 -Wno-unknown-pragmas -DNDEBUG Best regards, Jiyong Su -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] Impact of ignoring hydrogens

gt; > Best, > > -- > Dr. Matej Repic > Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational > Chemistry and Biochemistry SB - ISIC ­ LCBC BCH 4108 CH - 1015 Lausanne > > --

[gmx-users] Impact of ignoring hydrogens

Hello All I am doing protein ligand MD to view the interactions and effect of ligand on protein structure. However the NMR structure of protein encountered some warnings and considering that, i ignored hydrogens by -ignh. I believe that the hydrogen bonding might reduce due to this action. Is

Re: [gmx-users] Protein-Ligand Interactions

Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of su sun.i...@gmail.com Sent: Thursday, August 06, 2015 5:23 PM To: gmx-us...@gromacs.org Subject: [gmx-users] Protein

[gmx-users] Protein-Ligand Interactions

Hello I have posted this query already but in absence of any suggestion,i am posting it again. After completion of protein-ligand MD, I tried to visualize the trajectory in VMD.It shows only protein and my ligand is absent. To view hydrogen bond interactions between pro-lig, i have gmx hbond,

[gmx-users] Protein-Ligand

Hello I am confused about my MD results.According to Justin's tutorial of protein-ligand MD, i performed short 1ns md on my protein-ligand system. After completion, when i opened up the md.gro and md.xtc in VMD, it is only showing up protein.Ligand is absent from box. When i tried to view

[gmx-users] MD run complete but ligand not showing up

Hello I am confused about my MD results.According to Justin's tutorial of protein-ligand MD, i performed short 1ns md on my protein-ligand system. After completion, when i opened up the md.gro and md.xtc in VMD, it is only showing up protein.Ligand is absent from box. Also, no .trr file is

[gmx-users] Atom type SDMSO not found

Hello everyone I am doing protein-ligand simulation according to Justin's tutorial. After running gmx grompp command, i encountered following error: Fatal error: Atomtype SDMSO not found. Is this the force field matching problem? because i am not able to find out any such atom types in any of

Re: [gmx-users] itp file not found

Dear James I think you din't give Justin a chance to reply  I mean you solved your query yourself. Rather, i was waiting for Mark's sarcastic comment  Well, i had the same problem but like you, it was solved. Best Regards Suniba Sent from my iPhone On 24-Jul-2015, at 7:05 am, James Lord

Re: [gmx-users] pdb2gmx error residue not found in residue topology database

...@maillist.sys.kth.se] On Behalf Of su Sent: Wednesday, July 08, 2015 11:26 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] pdb2gmx error residue not found in residue topology database How you converted the gaussian file into .pdb? Because once i did the same and suffered from some missing co

[gmx-users] Simulating Peptides

Hello I am going to simulate the Unfolding process of Amyloid beta peptide (PDB ID 1IYT) and the fibrillar structure as well, Alone and with ligands. Can anyone suggest a good tutorial or reference article for the same? For the papers that i studies, none has explained the MD process. Regards

Re: [gmx-users] Simulating Peptides

(as far as I am aware), just its hydrophobic part (vide PDB 2beg (mono), 2lmn (di) and 2lmp (tri)). You will probably find some refs in under this pdb's. Best, Mateusz On 07/08/2015 03:35 PM, su wrote: Hello I am going to simulate the Unfolding process of Amyloid beta peptide (PDB ID

Re: [gmx-users] pdb2gmx error residue not found in residue topology database

How you converted the gaussian file into .pdb? Because once i did the same and suffered from some missing co ordinates. Sent from my iPhone On 08-Jul-2015, at 11:16 pm, Peter Stern peter.st...@weizmann.ac.il wrote: Look at the file: residuetypes.dat in the ../top/ directory of your

[gmx-users] System Problem

Hello everyone I am using Gromacs 5.0 for running a tutorial. The tutorial is successfully done and i have obtained .gro file. I am a beginner and do not have idea how to visualize this file in pymol? can anyone help in this regard? Secondly, this may be a partition problem but if anyone knows,

Re: [gmx-users] Bootstrap error

for recent versions of GROMACS, so get the latest gcc for your Ubuntu version while you are doing that. Mark On Mon, Apr 13, 2015 at 6:54 PM, su sun.i...@gmail.com wrote: Dear All I am new to Gromacs and i am trying to install it in Ubuntu. I am getting following error while using the command

[gmx-users] Bootstrap error

Dear All I am new to Gromacs and i am trying to install it in Ubuntu. I am getting following error while using the command ./configure in cmake step. C compiler on this system is: cc Error when bootsratpping CMake: Cannot find appropriate C++ compiler on this system. Please specify one using

[gmx-users] Installation Error

Dear All I am trying to install Gromacs on ubuntu. I have followed the quick and dirty tutorial but when i untar the gromacs-4.6.4.tar.gz file it gives error that no such file ir directory. File is located in the system , i dont know why it is happening. please help Regards Su Sent from my