[gmx-users] dssp 3.1.4
Good day, I have recently downloaded the latest dssp version and with the mkdssp executable file as I type chmod +x dssp and run this code : gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg -tu ns the process starts but no output is created after even 1 day my Gormacs version is 2019.3 and even earlier versions of dssp does not work and give me the same result. Till now I have tested this process on 3 computers having GROMACS 2019.3 on them. Can someone help me with this issue? Many thanks. -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] dssp version of gromacs 2019.3
Good day, I have downloaded the latest version of DSSP from the site : https://swift.cmbi.umcn.nl/gv/dssp/ <https://www.researchgate.net/deref/https%3A%2F%2Fswift.cmbi.umcn.nl%2Fgv%2Fdssp%2F> however as I downloaded and extract the package I see it is named hssp 1.3.4 and the codes are different from dssp that determines the secondary structures in gromacs using gmx do_dssp! can somebody help me on this issue and send me the latest version of DSSP for gromacs 2019.3 so that I can make it executable and do my task. As I run it with older version of dssp it reads the code and starts reading the frames, however even after 2 hours nothing happens and the frame is still zero! Many thanks -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] do_dssp
Good day, I am using do_dssp to determine the secondary structure of my protein however when I run my code : gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg -tu ns I encounter this, and after several minutes the reading time frames is still ZERO!! I have already did chmod +x dssp in > '/usr/local/bin/dssp *Here is the message after running the code:* -i ddub26pK 2>/dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddub26pK to ./#ddub26pK.1# Thanks. -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science an* Selected 1: 'Protein' There are 122 residues in your selected group dssp cmd='/usr/local/bin/dssp -i ddub26pK 2>/dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddub26pK to ./#ddub26pK.1# -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Young's modulus
Good day, How can I calculate Young and shear modulus using GROMACS package? Thanks. -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] acidic pH simulation
Good day, I want to simulate the behavior of my protein at different pH conditions including *acidic and basic values*. Can somebody suggest what should I do to change the pH of my system? Thanks -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] CA ions
Good day, I want to simulate my protein in gromacs and in this simulation I need to add a certain concentration of CA ions to my system. However, I have no idea about how to do this so first I have to neutralize my system and then need to add the needed CA ions which act as binding agents* (necessary factor in experiments) *in my protein. I have heard that with -neutral and -conc for adding the certain concentration I can do this thing. I would appreciate it if somebody can help me with this issue. Thanks. -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] npt.tpr protein-lig
Good day, I have generated npt.tpr for my protein ligand and changed my npt.mdp file according to the suggestions by GROMACS for using Brendsen and h-bonds for constraints finally I encounter this NOTE which I think will cause further problems in my md run : NOTE 1 [file topol.top, line 18260]: The bond in molecule-type UNL between atoms 6 C5 and 7 C6 has an estimated oscillational period of 1.8e-02 ps, which is less than 10 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option. Number of degrees of freedom in T-Coupling group Protein_UNL is 4960.82 Number of degrees of freedom in T-Coupling group Water_and_ions is 77850.18 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm I would appreciate it if someone tells me what I need to do with my system I think it may be related to the time step of my simulaiton and frames as I searched the similar issues. thanks -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] toluene as a slovent
Hello, I have downloaded the toluene pdb file and want to use it as solvent in GROMACS rather than the water molecules. I have added toluene as a molecule using gmx solvate -cs toluene.gro however, in the next steps, it is not added to the topol.top file and I cannot go-ahead to the next steps of simulation. I'd be grateful if someone can help me with this issue as I have not tried other solvents rather than water before. Thanks. On Sun, Dec 1, 2019 at 4:04 PM Iman Katouzian wrote: > Hello, > > I have downloaded the toluene pdb file and want to use it as solvent in > GROMACS rather than the water molecules. I have added toluene as a molecule > using gmx solvate -cs toluene.gro however, in the next steps, it is not > added to the topol.top file and I cannot go-ahead to the next steps of > simulation. I'd be grateful if someone can help me with this issue as I > have not tried other solvents rather than water before. > > Thanks. > > -- > > *Iman Katouzian* > > *Ph.D.** candidate of Food Process Engineering* > > *Faculty of Food Science and Technology* > > *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* > -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Toluene .rtp
Hello, I wonder if somebody can help me where I can find the parameters for *toluene *solvent so that I can add it to the .rtp file for addition to my protein system as for the solvent I want to add this type and NOT water molecules. Thanks -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] protein_ligand error NVT
Good day. I have encountered a problem in my protein-ligand simulation as after the energy minimization step, when I run the gmx mdrun -deffnm nvt I encounter the error segmentation faiulire core dumped : step 1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Back Off! I just backed up step1b.pdb to ./#step1b.pdb.8# Back Off! I just backed up step1c.pdb to ./#step1c.pdb.8# Wrote pdb files with previous and current coordinates *Segmentation fault (core dumped)* Thanks. -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Pro-Lig Error
Hello, I have simulated a protein-ligand file and produced the ligand file by antechamber software using the Amber03 force field. All the stages in Gromacs were performed correctly without any error however when I ran this code : gmx grompp -f MDP/ions.mdp -c solv.gro -p topol.top -o ions.tpr I encounter this error: Fatal error: number of coordinates in coordinate file (solv.gro, 40906) does not match topology (topol.top, 40950) I just performed my simulation many times but I could not pass this error. Thanks -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cellulose topology file
Iman Katouzian 4:07 PM (23 minutes ago) to gromacs.org_gmx-users Good day. I have a pdb file for nanocellulose and as I run the first command in Gromacs using gmx pdb2gmx -f Cellulose.pdb I encounter the following error : Warning: Starting residue UN15 in chain not identified as Protein/RNA/DNA. This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add UN1 to residuetypes.dat if this was not correct. Disabling further warnings about unidentified residues at start of chain. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully It seems that Gromacs does not recognize the residues but in a recent paper the structure was run successfully in Gromacs and the run was OK. Could you please tell me what I'm doing wrong. Thanks -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cellulose topology file
Good day. I have a pdb file for nanocellulose and as I run the first command in Gromacs using gmx pdb2gmx -f Cellulose.pdb I encounter the following error : Warning: Starting residue UN15 in chain not identified as Protein/RNA/DNA. This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add UN1 to residuetypes.dat if this was not correct. Disabling further warnings about unidentified residues at start of chain. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully It seems that Gromacs does not recognize the residues but in a recent paper the structure was run successfully in Gromacs and the run was OK. Could you please tell me what I'm doing wrong. Thanks -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] ERROR: Failed to load the OptiX shared library.
Good day, After the installation of VMD in Linux ubuntu I encounter this error for my GPU and I yet could not fix it can someone help me fix this issue? the error is written below : info) No CUDA accelerator devices available. Warning) Detected X11 'Composite' extension: if incorrect display occurs Warning) try disabling this X server option. Most OpenGL drivers Warning) disable stereoscopic display when 'Composite' is enabled. Info) OpenGL renderer: AMD RV710 (DRM 2.50.0 / 4.15.0-55-generic, LLVM 8.0.0) Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS) Info) Full GLSL rendering mode is available. Info) Textures: 2-D (8192x8192), 3-D (512x512x512), Multitexture (8) OptiXRenderer) ERROR: Failed to load the OptiX shared library. OptiXRenderer)NVIDIA driver may be too old. OptiXRenderer)Check/update NVIDIA driver Aborted (core dumped) Thanks. -- *Iman Katouzian* *Ph.D.** candidate of Food Process Engineering* *Faculty of Food Science and Technology* *University of Agricultural Sciences and Natural Resources, Gorgan, Iran* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
