Re: [gmx-users] pdb generator
Hi Ali, thanks for you help. How can you distinguish between a C atom from residue XXX and another C atom from residue YYY when there are about 2000 atoms in the file. Did you write a script for that? If there doesnt exist a tool with a GUI to solve this then i will have to write my own builder. Cheers Momin Am 13.11.18 um 16:31 schrieb Ali Ahmed: well if you use Linux then you can use GVim to do highlight and do simple changes on one type only then use find and replace option. That what I do when I have more than one type. It needs one hour practice then you will be ok. Or you can write a script for such things. Best On Tue, Nov 13, 2018 at 9:15 AM Momin Ahmad wrote: Hi Ali, my problem is that there is not only one molecule but two different molecules which build up a crystaline structure. For example i have 10 XXX and 100 YYY in the .pdb file. Cheers Momin Am 13.11.18 um 16:12 schrieb Ali Ahmed: Hi, I use Avogadro and it is easy to change LIG to anything you want. I just use find and replace option which takes less than a minute. Best Ali On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad wrote: Hi, is there a tool where i can use for example a .cif file (or .xyz) file to generate a .pdb file with correct classification? For example Avogadro classifies all atoms as LIG and i cannot change it. Is there also another tool which can be used to generate large scale crystal structures with building blocks as input? Cheers Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] pdb generator
Hi Ali, my problem is that there is not only one molecule but two different molecules which build up a crystaline structure. For example i have 10 XXX and 100 YYY in the .pdb file. Cheers Momin Am 13.11.18 um 16:12 schrieb Ali Ahmed: Hi, I use Avogadro and it is easy to change LIG to anything you want. I just use find and replace option which takes less than a minute. Best Ali On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad wrote: Hi, is there a tool where i can use for example a .cif file (or .xyz) file to generate a .pdb file with correct classification? For example Avogadro classifies all atoms as LIG and i cannot change it. Is there also another tool which can be used to generate large scale crystal structures with building blocks as input? Cheers Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] pdb generator
Hi, is there a tool where i can use for example a .cif file (or .xyz) file to generate a .pdb file with correct classification? For example Avogadro classifies all atoms as LIG and i cannot change it. Is there also another tool which can be used to generate large scale crystal structures with building blocks as input? Cheers Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] specbonds
Hi, i have two different residues and i want a bond defines between them. I know i have to use the specbond.dat file but how do i implement the additional potentials like stretching/angles/dihedrals? Is it enough to just describe them in ffbonded.itp? Example: i have CH3 and NH as different residues and want a bond between C and N. For the topology i want also to define the parameters for the N-H bond, H-C-N/C-N-H angles. Sincerely Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Simulating crystal structures
Hello, is GROMACS able to simulate crystaline structures properly? I have two residues parametrized that build up the crystal structure. The unit cell is however cut off at the edges (periodicity). So the question is if i enable periodic boundry conditions will GROMACS be able to handle the edges properly (covalent bonds that end on the one side are continued on the other side)? And is it possible to tell GROMACS that the uncomplete residues in the corners/edges of the unit cell are just the already parametrized or do i have to create another residue entry for each edge/corner molecules? Thanks in advance Cheers Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] specbond
Hello, i parametrized two component of my metal-organic framework as modular building block. Each component has an entry in the .rtp file and pdb2gmx and grompp do work. Now i want to define bonds between both residues. In specbond.dat it is possible to do so but where do i put in the new force-field parameters for additional bonds, angles, dihedrals that are formed by the intermolecular bond? Kind regards Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Dihedral angles in crystaline structure
Hello, is anybody in this mailing list experienced in the parametrization of crystaline structures (i am working on metal organic frameworks) and is willing to answer some questions on dihedral angles? Kind regards Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Ionic bonds
Hello, is there a difference in the implementation of an ionic bond and a covalent bond? For example UFF gives parameters for both atoms i and j. The atoms i and j should form an ionic bond and UFF gives me the parameters for the strecthing and bending potential. But in the case of dihedrals i only have information for sp^2 and sp^3 bonds. So should i just take the i and j as a sp^2 bond because i have the parameters for it (there are no parameters for a sp^3 )? Cheers, Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Dihedral between non bonded atoms
Hi, is there a reason why gromacs demands parameters for dihedral angles that are not bonded? For example i,j, and k are bonded but l is not. The distance of k and l is about 2.7 Angstroem. How can i tell gromacs to ignore these dihedrals during pdb2gmx. I did no define a bond in the .rtp file. The .pdb i used for pdb2gmx is attached. Thanks in advance. Cheers, Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Force Field Parameters
Hi, i am trying to parametrize a Metal-Organic-Framework for later gromacs simulations. Does anybody have experience in deriving parameters like force constants completely from theory? I know that there are techniques doing it with DFT-calculations but i would like to know other methods as well to determine which one is best suited for my work. Cheers, Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Partial Charge precision
Hi, yeah i missed the charge group number. Thanks for reminding Cheers, Momin Am 28.05.2018 um 16:59 schrieb Justin Lemkul: On 5/28/18 10:34 AM, Momin Ahmad wrote: Hello, how many decimal digits are allowed in .rtp files for partial charges? i got this error: ## Using the Uff4mof force field in directory ./uff4mof.ff No file 'watermodels.dat' found, will not include a water model Reading benzene.pdb... Read 'BENZENE', 12 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 1 residues with 12 atoms chain #res #atoms 1 ' ' 1 12 All occupancies are one Opening force field file ./uff4mof.ff/atomtypes.atp Invalid format: [ atomtypes ] Atomtype 146 Reading residue database... (uff4mof) Opening force field file ./uff4mof.ff/bb.rtp --- Program: gmx pdb2gmx, version 2016.3 Source file: src/gromacs/gmxpreprocess/resall.cpp (line 489) Fatal error: in .rtp file in residue BDC at line: C1 C_1 -0.0313981005 ### I wrote down the whole number and did not round anything. That's way too many digits to have any practical use or meaning. I'd suggest rounding to -0.0314. The error is about the format of the line, not the precision of the value, so your .rtp entry is broken in some way (perhaps simply due to the absence of a charge group number, but it could be one of several things). -Justin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Partial Charge precision
Hello, how many decimal digits are allowed in .rtp files for partial charges? i got this error: ## Using the Uff4mof force field in directory ./uff4mof.ff No file 'watermodels.dat' found, will not include a water model Reading benzene.pdb... Read 'BENZENE', 12 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 1 residues with 12 atoms chain #res #atoms 1 ' ' 1 12 All occupancies are one Opening force field file ./uff4mof.ff/atomtypes.atp Invalid format: [ atomtypes ] Atomtype 146 Reading residue database... (uff4mof) Opening force field file ./uff4mof.ff/bb.rtp --- Program: gmx pdb2gmx, version 2016.3 Source file: src/gromacs/gmxpreprocess/resall.cpp (line 489) Fatal error: in .rtp file in residue BDC at line: C1 C_1 -0.0313981005 ### I wrote down the whole number and did not round anything. Cheers, Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Force Fields
Hi Mark, thanks for the answer. My thought was if i get all bonded parameters and force constants through DFT-calculations i should be able to choose my preferred potential equations. Or am i wrong because i am still using nonbonded data from UFF? Cheers Momin Am 25.04.2018 um 12:12 schrieb Mark Abraham: Hi, The parameters are strongly correlated to both the equations in which they work, and the other parameters in the force field alongside which they were parametrized. Many kinds of transfer simply will not work, and all of them need to be validated, e.g. by reproducing some previous computational or experimental result. Mark On Wed, Apr 25, 2018 at 11:50 AM Momin Ahmad wrote: Hi, i have a question regarding force fields (not gromacs related). In UFF (https://pubs.acs.org/doi/abs/10.1021/ja00051a040) the potential equations of angles and dihedrals are different than in gromacs. OBGMX just reparametrizes them to still use the data from UFF (https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.23049). My question would be what defines my dependence on the potential equations. If i take bonded parameters from DFT-calculations and use the nonbonded from UFF, am i allowed to just change potential equations or is this not allowed as i am still using data from UFF (nonbonded). Bonded stretch potential and nonbonded potentials are the same (harmonic, lennard jones). Greets Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 <+49%20721%2060824286> E-Mail: momin.ah...@kit.edu -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Force Fields
Hi, i have a question regarding force fields (not gromacs related). In UFF (https://pubs.acs.org/doi/abs/10.1021/ja00051a040) the potential equations of angles and dihedrals are different than in gromacs. OBGMX just reparametrizes them to still use the data from UFF (https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.23049). My question would be what defines my dependence on the potential equations. If i take bonded parameters from DFT-calculations and use the nonbonded from UFF, am i allowed to just change potential equations or is this not allowed as i am still using data from UFF (nonbonded). Bonded stretch potential and nonbonded potentials are the same (harmonic, lennard jones). Greets Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Fw: Geometry Optimization for Metal organic Frame works
Hi, i am also simulating MOFs with gromacs and can say that OBGMX is not the best way to generate the topology file. It has many flaws but shows some ideas. I am currently creating my own forcefield using the UFF4MOF by M. Addicoat. You can have a look at it: https://pubs.acs.org/doi/abs/10.1021/ct400952t Greets, Momin Am 07.03.2018 um 14:25 schrieb Nagasree Garapati: Thank You Micholas I have created the topology files using initial input file in OBGMX and it shows that there are 20 unique bond terms, out of which there are 3 bonds between the metal ion and the N2 in linker. However, when I tried to create topolgies using the optimized final output (final.gro) file in OBGMX, nothing is created I have empty files for both .top and .itp files. I believe there is something wrong with the topology files, but I am not able to figure out where is the mistake. Any suggestions ? Thank You With Regards Nagasree Garapati Research Assistant Professor Dept of Chemical and Biomedical Engineering West Virginia University PO Box 6102 Morgantown, WV 26506-6102 304 293-5028(O) 304 276-3674(M) -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Creating Forcefield without ffbonded.itp
Hello, is it possible to include all needed bonded parameters (bond lenght, bond angle,...) in the .rtp file and ignore the ffbonded.itp completely? Such case would be if a molecules structure has specified parameters which only fit said structure. According to the manual bond length and angle should be possible but the force constants are not mentioned. Greets, Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Tool for molecule drawing
Hello, does anybody know of a software (with gui!) that allows to draw and assign residue names atom per atom? For example display a molecule with the gui and clicking on the atoms to define the residue name. Thanks in advance, Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Usage of GROMACS
Hello Micholas, thank you for the fast reply. Unfortunately i have bad experience with x2top and is no option for me (considering crystalline structures). I might have to look for other options. Cheers Momin Am 04.12.2017 um 14:40 schrieb Smith, Micholas D.: Hi Momin, Unfortunately, crystalline structures are, as you have experienced, not the easiest thing to simulate using gromac's system building tools. Typically, people working on MOFs, clays, general polymers, and other non-biological systems use something like LAMMPS (or DL_Poly like you have already noted). That being said, it isn't impossible to use gromacs for these types of systems, it just takes a bit of time. One tool that can be useful for these types of systems with gromacs, however, is the x2top tool. It is far from perfect, but it can get you started in the right direction. -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Momin Ahmad Sent: Monday, December 04, 2017 8:27 AM To: gmx-us...@gromacs.org Subject: [gmx-users] Usage of GROMACS Hello, is GROMACS meant to be used for simulations of crystaline structures (Metal Organic Frameworks, porous materials, minerals, ...)? Almost every paper working on MD simulations with said structures use DL_Poly or other software. So my question would be is there a community that uses GROMACS to simulate crystaline structures? Porting .cif files to pdb and then trying to run pdb2gmx with writing a .rtp file is very time consuming. Cheers Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Usage of GROMACS
Hello, is GROMACS meant to be used for simulations of crystaline structures (Metal Organic Frameworks, porous materials, minerals, ...)? Almost every paper working on MD simulations with said structures use DL_Poly or other software. So my question would be is there a community that uses GROMACS to simulate crystaline structures? Porting .cif files to pdb and then trying to run pdb2gmx with writing a .rtp file is very time consuming. Cheers Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Simulating Metal-Organic Frameworks
Hello, does anybody have experience in simulating Metal-Organic Frameworks with gromacs? If so, i would like to ask some questions regarding (e.g.: .rtp files, force-fields) Best, Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Merging different topology files
Hi Justin, could you provide me a link to some tutorials that focus more on the program structure than on the results of simulations? I did some protein simulation tutorials that did not really help me in understanding the software itself. Big thanks in advance. Cheers, Momin Am 08.09.2017 um 13:42 schrieb Justin Lemkul: On 9/8/17 5:50 AM, Momin Ahmad wrote: Thank you for your help. I already did that but i get a weird error that i can not solve. I attached the topology files and the error message. Maybe the numbering of the residues has to be changed? Thanks in advance. You have lots of missing parameters, which means your force field doesn't know how to represent these molecules. You are also missing several bonded interactions in your ammonia topology, so the simulation won't be stable. As to the last fatal error, your [molecules] directive doesn't actually specify how many molecules you have: [molecules] AMMONIA METHANE There need to be actual numbers here. Please go back and do some basic GROMACS tutorials and reading in the PDF manual (particularly Chapter 5) to understand topology format before trying to do something like this. It's very easy to make lots of mistakes, some obvious and some not. -Justin Cheers, Momin Am 07.09.2017 um 21:08 schrieb Justin Lemkul: On 9/7/17 10:19 AM, Momin Ahmad wrote: Hello all, is there a simple way to merge two or more topology files into one? I am trying to use grompp to set up a simulation but my solvation contains different molecules which have different .top files. I also tried creating a main topology file which includes the other two topologies but without success. Hope anyone knows how to solve this. The #include mechanism is the only way to do this. If you have two .top (system topology) files, then: 1. Remove any #include statement for a parent force field (i.e. the file with [defaults] in it) 2. Remove any [system] or [molecules] directive (you now have proper .itp format) 3. Remove any redundant #include statements (e.g. for water, ions) to avoid "moleculetype redefined" errors 4. Construct a new .top that #includes a parent force field, your two new .itp files, and has [system] and [molecules] directives. -Justin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Merging different topology files
Thank you for your help. I already did that but i get a weird error that i can not solve. I attached the topology files and the error message. Maybe the numbering of the residues has to be changed? Thanks in advance. Cheers, Momin Am 07.09.2017 um 21:08 schrieb Justin Lemkul: On 9/7/17 10:19 AM, Momin Ahmad wrote: Hello all, is there a simple way to merge two or more topology files into one? I am trying to use grompp to set up a simulation but my solvation contains different molecules which have different .top files. I also tried creating a main topology file which includes the other two topologies but without success. Hope anyone knows how to solve this. The #include mechanism is the only way to do this. If you have two .top (system topology) files, then: 1. Remove any #include statement for a parent force field (i.e. the file with [defaults] in it) 2. Remove any [system] or [molecules] directive (you now have proper .itp format) 3. Remove any redundant #include statements (e.g. for water, ions) to avoid "moleculetype redefined" errors 4. Construct a new .top that #includes a parent force field, your two new .itp files, and has [system] and [molecules] directives. -Justin :-) GROMACS - gmx grompp, 2016.3 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton FeenstraGerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios Karkoulis Peter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, version 2016.3 Executable: /usr/local/bin/gmx Data prefix: /usr/local Working dir: /home/momin/work/click-chemistry/simulation Command line: gmx grompp -f minim.mdp -c system_solv.gro -p topol.top -o system.tpr Back Off! I just backed up mdout.mdp to ./#mdout.mdp.14# NOTE 1 [file minim.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 61641030 Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations ERROR 1 [file methane_custom.itp, line 16]: No default Bond types ERROR 2 [file methane_custom.itp, line 17]: No default Bond types ERROR 3 [file methane_custom.itp, line 18]: No default Bond types ERROR 4 [file methane_custom.itp, line 19]: No default Bond types ERROR 5 [file methane_custom.itp, line 23]: No default Angle types ERROR 6 [file methane_custom.itp, line 24]: No default Angle types ERROR 7 [file methane_custom.itp, line 25]: No default Angle types ERROR 8 [file methane_custom.itp, line 26]: No default Angle types ERROR 9 [file methane_custom.itp, line 27]: No default Angle types ERROR 10 [file methane_custom.itp, line 28]: No default Angle types WARNING 1 [file topol.top, line 18]: Too few parameters on line (source file /home/momin/gromacs-2016.3/src/gromacs/gmxpreprocess/toppush.cpp, line 2377) Excluding 3 bonded neighbours molecule type 'METHANE' WARNING 2 [file topol.top, line 19]: Too few parameters on line (source file /home/momin/gromacs-2016.3/src/gromacs/gmxpreprocess/toppush.cpp, line 2377) Excluding 3 bonded neighbours molecule type 'METHANE' --- Program: gmx grompp, version 2016.3 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 612) Fatal error: number of coordinates in coordinate file (system_solv.gro, 113) does not match topology (topol.top, 10) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- ; main topology file ; ; Include force-field #include "amber99sb-ild
[gmx-users] Fwd: Merging different topology files
weird, my email got cut off Weitergeleitete Nachricht Betreff:Merging different topology files Datum: Thu, 7 Sep 2017 16:19:29 +0200 Von:Momin Ahmad An: gmx-us...@gromacs.org Hello all, is there a simple way to merge two or more topology files into one? I am trying to use grompp to set up a simulation but my solvation contains different molecules which have different .top files. I also tried creating a main topology file which includes the other two topologies but without success. Hope anyone knows how to solve this. Best, Momin -- 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] Merging different topology files
Hello all, is there a simple way to merge two or more topology files into one? I am trying to use grompp to set up a simulation but my solvation contains different molecules which have different .top files. I also tried creating a main topology file which includes the other two topologies but without success. Hope anyone knows how to solve this. Best, Momin -- 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] Creating Custom .rtp files
I think the reason for the weird log is the "|&tee" command that lets you write the output of another command into a file. In the case of the error i could choose the forcefield before the error occurred. The methane was called "CH4" before, i just changed the names for troubleshooting. This time i did copy&paste manually. Files are attached. There are two comments that show the differences in the versions. Again: the two .rtp files for both versions are identical and the same .pdb file is used. Am 01.08.2017 um 20:42 schrieb Justin Lemkul: On 8/1/17 10:32 AM, Momin Ahmad wrote: please finde the files attached to this email: log-files for the 5.1.2 version and the 2016.3 version, also again the .rtp file and the .pdb file The screen output seems garbled to me, with the fatal error coming before the force field selection, and multiple locations being used. I can't figure out what's going on. Your .rtp needs to be in the force field directory that you choose, either locally (within the working directory) or system-wide (wherever that is installed). Note also that "CH4" and "CH41" are different, because one error indicates that pdb2gmx finds CH4 when your .rtp is clearly CH41. -Justin Am 01.08.2017 um 00:48 schrieb Justin Lemkul: On 7/31/17 7:47 AM, Momin Ahmad wrote: Hello, the .rtp file is located in the same directory as the force-field. When i type gmx gmx2pdb . then the log shows that the right path is considered and loads the needed .rtp fiels that already exist in the forc-field file. But my custom one is ignored. Please post the full screen output of pdb2gmx, including the force field selection. If your .rtp file is not being read, it is likely misformatted, in which case you should either write your new residue entries in an existing file or upload it to a file-sharing service so we can provide feedback. -Justin Greets Momin Ahmad Am 25.07.2017 um 16:34 schrieb RAHUL SURESH: On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad wrote: Hi, I created a custom .pdb file and the associated .rtp file for the force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for the 5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3 version is a local installation in my /home/user folder. The log shows the correct paths but does not consider my custom .rtp file. I would recommend to check whether the rtp file location and source where gmx you have installed match. Apart from that I do not think any error with version of Gromacs. Am i doing something wrong with the newer version? I added two simple files of my problem. Thanks in advance. Cheers Momin Ahmad Karlsruher Institut of Technology Germany -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx pdb2gmx, VERSION 5.1.2 Executable: /usr/bin/gmx Data prefix: /usr Command line: gmx pdb2gmx -f methane.pdb Select the Force Field: From '/usr/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp.
Re: [gmx-users] Creating Custom .rtp files
please finde the files attached to this email: log-files for the 5.1.2 version and the 2016.3 version, also again the .rtp file and the .pdb file Am 01.08.2017 um 00:48 schrieb Justin Lemkul: On 7/31/17 7:47 AM, Momin Ahmad wrote: Hello, the .rtp file is located in the same directory as the force-field. When i type gmx gmx2pdb . then the log shows that the right path is considered and loads the needed .rtp fiels that already exist in the forc-field file. But my custom one is ignored. Please post the full screen output of pdb2gmx, including the force field selection. If your .rtp file is not being read, it is likely misformatted, in which case you should either write your new residue entries in an existing file or upload it to a file-sharing service so we can provide feedback. -Justin Greets Momin Ahmad Am 25.07.2017 um 16:34 schrieb RAHUL SURESH: On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad wrote: Hi, I created a custom .pdb file and the associated .rtp file for the force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for the 5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3 version is a local installation in my /home/user folder. The log shows the correct paths but does not consider my custom .rtp file. I would recommend to check whether the rtp file location and source where gmx you have installed match. Apart from that I do not think any error with version of Gromacs. Am i doing something wrong with the newer version? I added two simple files of my problem. Thanks in advance. Cheers Momin Ahmad Karlsruher Institut of Technology Germany -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx pdb2gmx, VERSION 5.1.2 Executable: /usr/bin/gmx Data prefix: /usr Command line: gmx pdb2gmx -f methane.pdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat 1: TIP3P TIP 3-point, recommended 2: TIP4P TIP 4-point 3: TIP4P-Ew TIP 4-point optimized with Ewald 4: TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues) 5: SPC simple point charge 6: SPC/E extended simple point charge 7: None Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b All occupancies are one Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomty
Re: [gmx-users] Creating Custom .rtp files
Hello, the .rtp file is located in the same directory as the force-field. When i type gmx gmx2pdb . then the log shows that the right path is considered and loads the needed .rtp fiels that already exist in the forc-field file. But my custom one is ignored. Greets Momin Ahmad Am 25.07.2017 um 16:34 schrieb RAHUL SURESH: On Tue, 25 Jul 2017 at 5:58 PM, Momin Ahmad wrote: Hi, I created a custom .pdb file and the associated .rtp file for the force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for the 5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3 version is a local installation in my /home/user folder. The log shows the correct paths but does not consider my custom .rtp file. I would recommend to check whether the rtp file location and source where gmx you have installed match. Apart from that I do not think any error with version of Gromacs. Am i doing something wrong with the newer version? I added two simple files of my problem. Thanks in advance. Cheers Momin Ahmad Karlsruher Institut of Technology Germany -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] Creating Custom .rtp files
Hi, I created a custom .pdb file and the associated .rtp file for the force-field (amber99sb-ildn.ff). The command pdb2gmx works fine for the 5.1.2 version of gromacs but not for the 2016.3 version. The 2016.3 version is a local installation in my /home/user folder. The log shows the correct paths but does not consider my custom .rtp file. Am i doing something wrong with the newer version? I added two simple files of my problem. Thanks in advance. Cheers Momin Ahmad Karlsruher Institut of Technology Germany [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 3 1 1 3 10 ; Methane [ CH4 ] [ atoms ] C C-0.240 1 H1 H 0.060 1 H2 H 0.060 1 H3 H 0.060 1 H4 H 0.060 1 [ bonds ] C H1 C H2 C H3 C H4 -- 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.
