Re: [gmx-users] Topology file

On 10/17/18 6:25 PM, Mahdi Sobati Nezhad wrote: thanks Justin for your helps. the pdb2gmx make posre_chain_A.itp but don't write any thing about it in my topol.top!!! Can I add it in my topol.top file?! And what's its template for it?! If pdb2gmx completed successfully, it's there. Check

Re: [gmx-users] Topology file

thanks Justin for your helps. the pdb2gmx make posre_chain_A.itp but don't write any thing about it in my topol.top!!! Can I add it in my topol.top file?! And what's its template for it?! On Fri, 5 Oct 2018 17:08 Justin Lemkul, wrote: > > > On 10/4/18 6:53 PM, Mahdi Sobati Nezhad wrote: > >

Re: [gmx-users] Topology file

Thanks rose for your help. so for ligand and protein interaction its better that I use position restraints On Wed, 10 Oct 2018 17:07 rose rahmani, wrote: > First, i think it's better to ask WHY > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > That's why people use position

Re: [gmx-users] Topology file

First, i think it's better to ask WHY http://www.gromacs.org/Documentation/How-tos/Position_Restraints That's why people use position restraints. About WHEN, sometimes your molecule behavior is different in box. For instance you study the interaction of your molecule with surface. So the

Re: [gmx-users] Topology file

Thanks rose. Can you tell me more about which cases I should use position restrictions?! Thanks On Fri, 5 Oct 2018 10:33 rose rahmani, wrote: > Hi, > > It depends on you, wheter you want to put position restriction on your > molecule you should add posre.itp to topol.top or not. > But whenever

Re: [gmx-users] Topology file

On 10/4/18 6:53 PM, Mahdi Sobati Nezhad wrote: Hello Gromacs users. When I use pdb2gmx the Gromacs make pores.itp but in my topol.top there is no any porse.itp What can I do?! Do it's important that porse.itp should be in topol.top or its enough that pdb2gmx make porse.itp?! pdb2gmx writes

Re: [gmx-users] Topology file

Hi, It depends on you, wheter you want to put position restriction on your molecule you should add posre.itp to topol.top or not. But whenever you use define=-DPOSRES in your .mdp file, GROMACS can read posre.itp files in topol.top an apply position restriction to molecule. Rose On Fri, 5 Oct

[gmx-users] Topology file

Hello Gromacs users. When I use pdb2gmx the Gromacs make pores.itp but in my topol.top there is no any porse.itp What can I do?! Do it's important that porse.itp should be in topol.top or its enough that pdb2gmx make porse.itp?! Thanks -- Gromacs Users mailing list * Please search the archive

[gmx-users] Topology file.

Hello everyone I use Gromacs 18.3. when I use the command "gmx pdb2gmx -f protein.pdb -o protein.gro" it makes a topology file. But this topology haven't "posre_Chain _A.itp" or any other posre in part "; Include chain topologies" im confused, that what is wrong?! Do I can add this posre parts

Re: [gmx-users] topology file

On 5/27/18 3:30 PM, mostafa paknia wrote: hi i need to build just one topology file for two items one drug and one carbon nanotube (as drug carrier) how can i do that? The CNT topology can be built with x2top. Anything else has to be parametrized with online servers or with whatever

Re: [gmx-users] topology file

Concatenate the drug and the CNT into a songle file by using cat ( see multiple protein in a box) renumber the combined gro... then take pdb from the gro file and use it as the initial structure.. put in any topology building server On Mon, 28 May 2018, 1:00 am mostafa paknia,

[gmx-users] topology file

hi i need to build just one topology file for two items one drug and one carbon nanotube (as drug carrier) how can i do that? -- 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

[gmx-users] Topology file

Dear all, I want to create a topol.top file for Silica slab for which the force fields parameters are available in literature as well as in the lammps.data file which works fine in lammps (below links). The slab has in general 2184 atom including two types of O atom(OS in surface part and OB in

[gmx-users] Topology file for amino acid

Hi, I want to add NME and ACE terminals to zwitterionic amino acid like threonine and then make an input topology file for GROMACS(.itp file) to be compatible with (AMBER99 ff in) GROMACS. I have tried many tutorials like( http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-nonstandard/) but

Re: [gmx-users] topology file error

On 2/19/18 5:55 AM, sp...@iacs.res.in wrote: Hii all I have prepared the topology file for urea molecule in AMBER99sb-ildn force field taking the parameters from ffbonded.itp and  ffnonbonded.itp available in AMBER folder. After simulation the urea molecule is somewhat distorted. The N-H

[gmx-users] topology file error

Hii all I have prepared the topology file for urea molecule in AMBER99sb-ildn force field taking the parameters from ffbonded.itp and  ffnonbonded.itp available in AMBER folder. After simulation the urea molecule is somewhat distorted. The N-H bond is tilted. Please suggest me how to solve this

Re: [gmx-users] Topology file of molecule

Dear Vytautas and Justin, Thank you both for the help. I will try to perform some dihedral scans of small and simple molecules. Best regards, Krzysztof 2017-12-04 15:24 GMT+01:00 Justin Lemkul : > > > On 12/4/17 5:31 AM, Krzysztof Kolman wrote: > >> Dear Justin, >> >> Since

Re: [gmx-users] Topology file of molecule

Dear Justin, Since you last answer, I have been trying to find some description how to perform dihedrals scans using some QM software and Gromacs. I have found out that it used to be some QM software implemented in Gromacs (Orca) but this implementation is not developed anymore and it does not

Re: [gmx-users] Topology file of molecule

Dear Magnus and Justin, Thank you very much for your help. Kind regards, Krzysztof 2017-11-23 13:55 GMT+01:00 Justin Lemkul : > > > On 11/23/17 7:51 AM, Magnus Lundborg wrote: > >> Dear Krzysztof, >> >> I wouldn't be too worried about the fact that GAFF parameters have been >>

Re: [gmx-users] Topology file of molecule

On 11/23/17 7:51 AM, Magnus Lundborg wrote: Dear Krzysztof, I wouldn't be too worried about the fact that GAFF parameters have been used for proper and improper torsion angles. It happens quite a lot with the OPLS-AA forcefield. But as always, it is good to verify that the topology behaves

Re: [gmx-users] Topology file of molecule

Dear Krzysztof, I wouldn't be too worried about the fact that GAFF parameters have been used for proper and improper torsion angles. It happens quite a lot with the OPLS-AA forcefield. But as always, it is good to verify that the topology behaves as expected. Unfortunately there is no

[gmx-users] Topology file of molecule

Dear Gromacs Users, I would like to perform a simulation of adsorption of 3,4-Dihydroxybenzoic acid (34DHBA) on silica surface using the OPLS-AA forcefield. I created topology files for the silica surface based on the information found in papers describing simulations of quartz (Wensink 2000 -

[gmx-users] Topology file (type A type B format) for free energy calculation of bond breaking

Dear Gromacs Users I wish to calculate free energy simulation in which I wish to break bond within a molecule from state A to state B. If I use bond type 6 to define that bond in the molecule then i think it should not generate exclusions (as stated in the manual of Gromacs version 5.1.2,

[gmx-users] topology file with virtual site for an asymetric linear molecule

Dear all, I would like to use the virtual site capability of GROMACS to construct the topology of an asymmetric linear molecule (say SeCN). Does somebody have an example of topology file for a similar molecule to share with me? Thank you Stéphane -- Gromacs Users mailing list * Please

Re: [gmx-users] Topology file and itp file

awesome :) Thank you! *Lan Hoa* 2017-04-23 20:15 GMT-05:00 Justin Lemkul : > > > On 4/22/17 10:39 PM, lan hoa Trinh wrote: > >> Dear Justin, >> I am assessing based on a time series. You are right :), even I used the >> same topology file, the change over time of the potential

Re: [gmx-users] Topology file and itp file

On 4/22/17 10:39 PM, lan hoa Trinh wrote: Dear Justin, I am assessing based on a time series. You are right :), even I used the same topology file, the change over time of the potential energy is still different. It is good to know ^&^ . All the information you provided are very helpful. Ok,

Re: [gmx-users] Topology file and itp file

Dear Justin, I am assessing based on a time series. You are right :), even I used the same topology file, the change over time of the potential energy is still different. It is good to know ^&^ . All the information you provided are very helpful. Ok, let me try to express what I 've understood so

Re: [gmx-users] Topology file and itp file

On 4/22/17 9:06 PM, lan hoa Trinh wrote: Dear Justin, I don't understand what you meant by saying MD is chaotic. You mean about velocity? I know that when we generate velocity based on Boltzmann distribution, we have to generate random number. However, what we call random numbers is not

Re: [gmx-users] Topology file and itp file

Dear Justin, I don't understand what you meant by saying MD is chaotic. You mean about velocity? I know that when we generate velocity based on Boltzmann distribution, we have to generate random number. However, what we call random numbers is not actually "random" because they are obeying

Re: [gmx-users] Topology file and itp file

On 4/20/17 4:37 PM, lan hoa Trinh wrote: Dear Mark, I equilibrated my system in NVT, and then plot the potential energy. However the potential energy created with the two topology is not match. Thanks in advance, MD is chaotic, and even identical topologies will yield different results. If

Re: [gmx-users] Topology file and itp file

Dear Mark, I equilibrated my system in NVT, and then plot the potential energy. However the potential energy created with the two topology is not match. Thanks in advance, Best regards, *Lan Hoa* 2017-04-20 14:25 GMT-05:00 Mark Abraham : > Hi, > > How are you assessing

Re: [gmx-users] Topology file and itp file

Hi, How are you assessing "different?" Mark On Thu, 20 Apr 2017 21:13 lan hoa Trinh wrote: > Dear All, > I am modelling a system of spherical beads (which I named as Fi) which only > repulsive each other. I would highly appreciate if some one can have a look > at the

[gmx-users] Topology file and itp file

Dear All, I am modelling a system of spherical beads (which I named as Fi) which only repulsive each other. I would highly appreciate if some one can have a look at the following topology which I created: (ficoll1.top) [ defaults ] ;nbfunc comb-rule gen-pairs 1 1 no [

Re: [gmx-users] topology file construction

On 3/19/17 10:02 AM, abhisek Mondal wrote: Hi, I'm using following topology configuration for the above said heteroatom: 1OM 1 ANP O1G 1 -0.348 15.9994 2 P 1 ANP PG 10.971 30.9738 3OM 1 ANP O2G 1 -0.348

Re: [gmx-users] topology file construction

Hi, I'm using following topology configuration for the above said heteroatom: 1OM 1 ANP O1G 1 -0.348 15.9994 2 P 1 ANP PG 10.971 30.9738 3OM 1 ANP O2G 1 -0.348 15.9994 4OM 1 ANP O3G

[gmx-users] topology file construction

Hi, I'm trying to perform a protein-ligand MD run. But could not being able to construct a reliable topology file of the ligand. I've tried the PRODRG server but charges comes out so messed up. If I set uniform charges to same kind of atoms then also how can I validate if my ligand is

Re: [gmx-users] topology file

On 1/23/17 2:17 PM, RAHUL SURESH wrote: Dear Justin if I want to run just my ligand, is that possible.? Sure. Treat it like any other solute. You have a topology (that's the hard part), so now you just have to solvate it and go using all the normal tools. -Justin On Mon, 23 Jan 2017

Re: [gmx-users] topology file

Dear Justin if I want to run just my ligand, is that possible.? On Mon, 23 Jan 2017 at 11:35 PM, Justin Lemkul wrote: > > > > > On 1/23/17 12:01 PM, RAHUL SURESH wrote: > > > Hey Mark sorry for the inconvenience I have caused you. CYSh file was > just > > > for an example. > > >

Re: [gmx-users] topology file

On 1/23/17 12:01 PM, RAHUL SURESH wrote: Hey Mark sorry for the inconvenience I have caused you. CYSh file was just for an example. And now I have generated the itp file using topolgen. I would like to run MDS on this particular molecule alone with any protien. What should I do for that.

Re: [gmx-users] topology file

Hey Mark sorry for the inconvenience I have caused you. CYSh file was just for an example. And now I have generated the itp file using topolgen. I would like to run MDS on this particular molecule alone with any protien. What should I do for that. Thank you. On Mon, 23 Jan 2017 at 8:21 PM,

Re: [gmx-users] topology file

Hi, There's not enough information here for anyone to help you (and you can't attach files to send to the list). Why didn't you find the generated topologies useful? Why do you care about CYSH? Mark On Mon, Jan 23, 2017 at 10:46 AM RAHUL SURESH wrote: > I have tried

[gmx-users] topology file

I have tried Ligpargen to generate topology for a molecule and I dont find it useful. And totally unaware how to use topolgen or topolbuild. Now I am trying to craft my topology manually. I would like to get some guidances. [ CYSH ] [ atoms ] Nopls_238 -0.500 1 Hopls_241

[gmx-users] topology file format

Dear Grimaces Users, I have a simple question about topology file format. What does "funct" mean in [ bonds ], [ angles ], and [ dihedrals ] terms? Would you please link me where I can find the topology file format meaning? Thank you. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Topology file for serotonin (5-HT)

On 7/27/15 1:03 AM, Ganesh Shahane wrote: Hi Justin, Yes. I tried the same, but during the preparation of the .tpr file using grompp it gives an error saying No default proper dihedral types for 3 dihedral angles which are not present in the ffbonded.itp of the charmm36 force-field. These 3

Re: [gmx-users] Topology file for serotonin (5-HT)

use swissparam server, http://swissparam.ch/ On Mon, Jul 27, 2015 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/27/15 1:03 AM, Ganesh Shahane wrote: Hi Justin, Yes. I tried the same, but during the preparation of the .tpr file using grompp it gives an error saying No default

Re: [gmx-users] Topology file for serotonin (5-HT)

Hi Justin, Yes. I tried the same, but during the preparation of the .tpr file using grompp it gives an error saying No default proper dihedral types for 3 dihedral angles which are not present in the ffbonded.itp of the charmm36 force-field. These 3 dihedrals consist of atoms that encompass the

Re: [gmx-users] Topology file for serotonin (5-HT)

On 7/23/15 2:10 AM, Ganesh Shahane wrote: Dear Gromacs Users, I am looking forward to performing some simulations of a receptor bound to serotonin (also known as 5-HT). Does anybody have the .itp file of serotonin for the charmm27 or charmm36 force field? Thank you! It's very

[gmx-users] Topology file for serotonin (5-HT)

Dear Gromacs Users, I am looking forward to performing some simulations of a receptor bound to serotonin (also known as 5-HT). Does anybody have the .itp file of serotonin for the charmm27 or charmm36 force field? Thank you! -- Best Regards, Ganesh Shahane -- Gromacs Users mailing list *

Re: [gmx-users] Topology file for Fullerene with OPLS_AA force field

For fullerenes, follow http://www.webcitation.org/66u2xJJ3O and use x2top to build the topology based on OPLSAA. Alex On Wed, Apr 15, 2015 at 12:51 AM, saeed poorasad s_poora...@yahoo.com wrote: Hi Gromacs users , I want to have a system with one C60 and about 1000 water molecules .I tried

Re: [gmx-users] Topology file for Fullerene with OPLS_AA force field

it's very much similar creating topology for CNT using g_x2top. You can search mailing list for that. Recently I have published a paper on fullerene water systems. http://www.tandfonline.com/doi/abs/10.1080/08927022.2014.998212#.VTKritzF8wA if you any problem you can contact me. Thanks Abhijit

[gmx-users] Topology file for Fullerene with OPLS_AA force field

Hi Gromacs users ,  I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use

[gmx-users] topology file from glycam/gaff to gromacs

Dear Gromacs user , i am a new user to gromacs and i am planning to run an MD for sugar system with nanoatoms in gromacs, i will use glycame force field for sugar and gaff force field for the other, I have the following question about the topology file: 1-i produced the top file that is

Re: [gmx-users] Topology file

Hi Michelle, You should only change the moleculetype definition. Delete the pairs/bonds/angles/dihedrals sections there, so you're only left with the atom listing and the position restraints. Cheers, Tsjerk On Jan 2, 2015 9:32 PM, Aranha, Michelle mara...@vols.utk.edu wrote: Hi, I wanted

[gmx-users] Topology file

Hi, I wanted to create a topology file without the bonds, angles and dihedrals for a CNT fixed in space using position restraints. I use the g_x2top program for building the topology. My understanding was that if I comment out the #include ffbonded.itp in the forcefield.itp file. I should

Re: [gmx-users] topology file

On 6/25/14, 12:52 AM, Andy Chao wrote: Hi, I have a few technical questions regarding creating the topology file by using the command g_x2top. I would like to use the following GROMACS's command: g_x2top -f device.gro -ff oplsaa -o device.top to convert the .gro file to .top. The problem

[gmx-users] topology file

Hi, I have a few technical questions regarding creating the topology file by using the command g_x2top. I would like to use the following GROMACS's command: g_x2top -f device.gro -ff oplsaa -o device.top to convert the .gro file to .top. The problem that I have is that the force field for

[gmx-users] topology file

I create a parallel job file with the following content #$ -N prep66 #$ -pe openmpi* 12 #$ -cwd #$ -q medium* mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/editconf_mpi -f 66.pdb -o cnt.gro -bt cubic -box 5 5 5 -c mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/g_x2top_mpi -f cnt.gro -o cnt.top

Re: [gmx-users] topology file

On 3/19/14, 2:22 PM, Michelle Aranha wrote: I create a parallel job file with the following content #$ -N prep66 #$ -pe openmpi* 12 #$ -cwd #$ -q medium* mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/editconf_mpi -f 66.pdb -o cnt.gro -bt cubic -box 5 5 5 -c mpirun -np 12

Re: [gmx-users] topology file for n-propanol

On Wed, Nov 20, 2013 at 4:53 PM, Ehsan Sadeghi es...@sfu.ca wrote: Thanks Justin. Could you explain more? You meant that I don't need topology file for propanol? How about g_b, g_a, g_d values? You need a topology, but what I'm saying is that it is very easy to do. CH3 and CH2 groups are