Re: [gmx-users] Force field for urea and urea-TMAO mixture

Dear Ishrat, I recommend this article and references therein for TMAO + urea parameters: http://dx.doi.org/10.1021/jacs.7b11695. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational

Re: [gmx-users] Force field for urea and urea-TMAO mixture

Hi, The urea model of Lorna Smith ( https://pubs.acs.org/doi/abs/10.1021/jp030534x ) should be compatible with GROMOS force field. Best regards Alessandra On Wed, Mar 4, 2020 at 7:00 AM ISHRAT JAHAN wrote: > Dear all, > I want to do MD simulation of protein in urea and urea-TMAO mixture. Can >

[gmx-users] Force field for urea and urea-TMAO mixture

Dear all, I want to do MD simulation of protein in urea and urea-TMAO mixture. Can you suggest me which force field would be better for urea and urea tmao mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field as I have done the simulation of protein with this force field. Any

[gmx-users] Force field for urea and urea-TMAO mixture

Dear all, I want to do MD simulation of protein in urea and urea-TMAO mixture. Can you suggest me which force field would be better for urea and urea tmao mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field as I have done the simulation of protein with this force field. Any

[gmx-users] Force field

Dear Gmx Experts, I would like to simulate hydroxyapatite with short peptides. I would like to use my own prepared surface which consists of a surface and a hole. I looked for some possible parameters. INTERFACE force field is compatible with GROMACS, which contains a number of small surfaces

Re: [gmx-users] force field for organometalic compound

Hi, You can use acpype to build the amber forcefield parameters. Each force field have corresponding servers which can make .tpr file for you. You can easily run simulation with that file. On Mon 10 Jun, 2019, 6:43 PM antonia vyrkou, wrote: > Dear all, > > I want to simulate an

[gmx-users] force field for organometalic compound

Dear all, I want to simulate an organometallic compound and how it affects an enzyme's function using Gromacs but I am having trouble finding suitable force field parameters. If would really appreciate any suggestions for a Gromacs compatible , Amber compatible force field Thank you Antonia --

Re: [gmx-users] Force field error

On 3/4/19 8:59 AM, Smith, Micholas D. wrote: Hi Swapnil Bhujbal, The parameters exist; however, the residue rtp file may not have entries for the phosphorylated residues. If you want to use pdb2gmx to you will need to add these residues into the rtp file associated with the force-field.

Re: [gmx-users] Force field error

Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Swapnil Bhujbal Sent: Monday, March 4, 2019 8:12:37 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Force field

Re: [gmx-users] Force field parameters not known

hey are space delimited. Regards, Peter -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Matthew Stoodley Sent: Thursday, February 21, 2019 12:59 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Force field parameters not kno

[gmx-users] Force field parameters not known

Hi, I am currently trying to perform a simulation on a chemical molecular machine but whenever I try and do the pdb2gmx command and select a force field it comes up with the message 'the residue DVHY is not recognised'. From my understanding what I should do is to update the residue in the

[gmx-users] Force Field for Polymers

I am new to gromacs. I am generating Polymers structures of varying chain length via Avogrado software. I am not sure about how to generate the .itp file. for a specific force field, in my case say OPLSAA. Also in case my polymer is a poly electrolyte how do I assign charges or how do I let the

Re: [gmx-users] force field not found

...@maillist.sys.kth.se] On Behalf Of Alex Sent: Sunday, September 30, 2018 12:44 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] force field not found Yeah, if it is missing bonded parameters, you can always try to find something similar, at least with OPLS-AA -- don't really know about the other ff

Re: [gmx-users] force field not found

AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] force field not found Yeah, if it is missing bonded parameters, you can always try to find something similar, at least with OPLS-AA -- don't really know about the other ff. Alex On 9/29/2018 8:58 PM, paul buscemi wrote: > Alex, &g

Re: [gmx-users] force field not found

Yeah, if it is missing bonded parameters, you can always try to find something similar, at least with OPLS-AA -- don't really know about the other ff. Alex On 9/29/2018 8:58 PM, paul buscemi wrote: Alex, I wanted to practice some more with x2top using a simple CH3 -( CH2)14 -Ch3 pdb

Re: [gmx-users] force field not found

Alex, I wanted to practice some more with x2top using a simple CH3 -( CH2)14 -Ch3 pdb model. oplsaa works fine, but not 54a7 FF generating the erro “ cannot find forcefield for C “ Th two CH3’s do not cause the error found but the fourteen CH2’s. In the ffbonded.itp bond angle types i

Re: [gmx-users] Force field parameter

I have already mailed them... waiting for their reply.. On Sat, 7 Jul 2018, 11:22 pm Mark Abraham, wrote: > Hi, > > Your other good approach is to contact the authors to ask them to share > their methodology fully, ie force field files. > > Mark > > On Sat, Jul 7, 2018, 13:47 Soham Sarkar

Re: [gmx-users] Force field parameter

Hi, Your other good approach is to contact the authors to ask them to share their methodology fully, ie force field files. Mark On Sat, Jul 7, 2018, 13:47 Soham Sarkar wrote: > Dear All, > Can anyone please tell me, where from I get the parameters for > Osmotic, Kast, Netz force

Re: [gmx-users] Force Field for Small Molecule

On 6/19/18 4:35 PM, Wahl, David M wrote: Hello, I am working on a molecular dynamics simulation in GROMACS and am curious as to which force field will be the best to run a simulation on a small organic molecule containing carbon, nitrogen, oxygen and hydrogen. Through some research it

Re: [gmx-users] Force Field for Small Molecule

I think you should recalculate charged of atoms of that molecule, the other properties can used from GAFF URL: https://qvu.netlify.com/#/ On Wed, Jun 20, 2018 at 3:36 AM Wahl, David M wrote: > Hello, > > > I am working on a molecular dynamics simulation in GROMACS and am curious > as to which

Re: [gmx-users] Force Field for Small Molecule

​I think you should recalculate charged of atoms of that molecule, the other properties can used from GAFF -- 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] Force Field for Small Molecule

Hello, I am working on a molecular dynamics simulation in GROMACS and am curious as to which force field will be the best to run a simulation on a small organic molecule containing carbon, nitrogen, oxygen and hydrogen. Through some research it seems that the general Amber force field (gaff)

[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

Re: [gmx-users] force field parameters for Fe3O4?

On 4/13/18 6:26 AM, rose rahmani wrote: Hello, I use AMBER force field. So, how about periodic structures? like inorganic nanosheet and nanotubes? One would never attempt to do parametrization directly on a full, periodic structure, largely because (1) it's not possible/practical and (2)

Re: [gmx-users] force field parameters for Fe3O4?

Hello, I use AMBER force field. So, how about periodic structures? like inorganic nanosheet and nanotubes? Thank you so much On Fri, 13 Apr 2018, 14:50 Paul bauer, wrote: > Hello, > > this depends on the force field you are using. Some of them use > parameters from a

Re: [gmx-users] force field parameters for Fe3O4?

Hello, this depends on the force field you are using. Some of them use parameters from a QM optimization and partial charge calculation. But even then you need to be careful that the results from the QM are not just random numbers :) But I'm not sure myself how I would tackle something like

Re: [gmx-users] force field parameters for Fe3O4?

On Fri, 13 Apr 2018, 14:35 Paul bauer, wrote: > Hello, > > I would recommend that you check relevant publications for the > simulation of magnetite if people have tried to simulate it in solvent. > I could not find anything during a short search, but maybe you'll be >

Re: [gmx-users] force field parameters for Fe3O4?

Hello, I would recommend that you check relevant publications for the simulation of magnetite if people have tried to simulate it in solvent. I could not find anything during a short search, but maybe you'll be more successful. :) If there are no published parameters in the literature you will

[gmx-users] force field parameters for Fe3O4?

Dear gromacs users, I want to simulate a protein in different concentration of Fe3O4. How to obtain force field parameters of Fe3O4? Any help will highly be appreciated. Best, -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] force field parameters clashing

On 1/15/18 1:27 PM, Harsha Ravishankar wrote: Hello Justin, Thanks for the reply. I only make use of Charmm GUI to generate the membrane patch, as I need to orient my protein in a particular orientation. However when I made use of the .itp forcefield files in gmx grompp -f ions.mdp -c

Re: [gmx-users] force field parameters clashing

Hello Justin, Thanks for the reply. I only make use of Charmm GUI to generate the membrane patch, as I need to orient my protein in a particular orientation. However when I made use of the .itp forcefield files in gmx grompp -f ions.mdp -c solvate.gro -p topol.top -o ions.tpr I get errors stating

Re: [gmx-users] force field parameters clashing

On 1/15/18 9:45 AM, Harsha Ravishankar wrote: Dear All, I am a beginner with Gromacs and simulations and I want to simulate a membrane and protein complex with the membrane comprising of 5 different lipid molecules. The membrane was generated with Charmm-GUI and the appropriate Gromacs

[gmx-users] force field parameters clashing

Dear All, I am a beginner with Gromacs and simulations and I want to simulate a membrane and protein complex with the membrane comprising of 5 different lipid molecules. The membrane was generated with Charmm-GUI and the appropriate Gromacs parameters for the different lipids were also obtained.

Re: [gmx-users] Force field informations

Hi, There's lots of discussion in the reference manual, and also in the force field files themselves. Mark On Mon, Jan 8, 2018 at 4:28 PM Lara rajam wrote: > Dear GMX users > I would like to know where we would get the force field information in GMX > . > Like in NAMD the

Re: [gmx-users] Force field informations

>I would like to know where we would get the force field information in GMX The answer is obvious: read manual (chapter 4 I"nteraction function and force fields" and 4.10 "Force field"). The FF files are situated in /usr/share/gromacs/top (for my PC) and are transparent enouth. -- Gromacs

[gmx-users] Force field informations

Dear GMX users I would like to know where we would get the force field information in GMX . Like in NAMD the Topology and parm file tells the details of the atom labeling,charge,connectivity etc., Simillarly where I could see the Gromos force field insights. Please provide me links or tutorials

Re: [gmx-users] force field packages

Hi, Thanks for the tip, I brought the website back up. Most of the relevant force fields are in the repo, however. Mark On Mon, Dec 4, 2017 at 7:54 PM Zahedeh Bashardanesh wrote: > Hi, > > Does anybody know where else to get the reliable amber force field package > for

[gmx-users] force field packages

Hi, Does anybody know where else to get the reliable amber force field package for gromacs except from gromacs website? The webpage has been down since Saturday. Best, --- Zahedeh Bashardanesh, Ph.D. Candidate

Re: [gmx-users] force field / parameters for NADH, FMN

Hi Justin, just for testing, I applied cgenff_charmm2gmx.py with charmm36-nov2016.ff as it has the same CGenFF version: --Version of CGenFF detected in /usr/local/gromacs/share/gromacs/top/charmm36-nov2016.ff/forcefield.doc : 3.0.1 But I still get the same warnings and errors. Would you

Re: [gmx-users] force field / parameters for NADH, FMN

On 11/3/17 10:33 AM, Hermann, Johannes wrote: Hey Justin, thanks - again -  for your reply! Now I get duplicated parameters warnings and errors: WARNING 1 [file fmn.prm, line 5]:   Overriding Bond parameters.   old:  0.1295 405848 0.1295 405848  

Re: [gmx-users] force field / parameters for NADH, FMN

Hey Justin, thanks - again -  for your reply! Now I get duplicated parameters warnings and errors: WARNING 1 [file fmn.prm, line 5]:   Overriding Bond parameters.   old:  0.1295 405848 0.1295 405848   new: CG2R64    NG2D1 1   0.1414   

Re: [gmx-users] force field / parameters for NADH, FMN

On 11/3/17 8:17 AM, Hermann, Johannes wrote: Dear Justin, thanks for the hint with the CHARMM-formatted topology and parameter files! That is great help! I had a different atom number compared to NAI and NADH because I had a different (non-physical) protonation state. The text drawing

Re: [gmx-users] force field / parameters for NADH, FMN

Dear Justin, thanks for the hint with the CHARMM-formatted topology and parameter files! That is great help! I had a different atom number compared to NAI and NADH because I had a different (non-physical) protonation state. The text drawing helped me a lot to figure out the few Nomenclature

Re: [gmx-users] force field / parameters for NADH, FMN

On 11/2/17 12:05 PM, Hermann, Johannes wrote: Dear Justin, dear all, thank you for your reply. I will test the web server when I have managed to generate the mol2 file for FMN. I had a look in the rtp file of charmm36 ff and I detected that there are three "NADHs": NAD1 , NAI, and NAD1.

Re: [gmx-users] force field / parameters for NADH, FMN

Dear Justin, dear all, thank you for your reply. I will test the web server when I have managed to generate the mol2 file for FMN. I had a look in the rtp file of charmm36 ff and I detected that there are three "NADHs": NAD1 , NAI, and NAD1. NAI is the pdb 3 letter code for the reduced form

Re: [gmx-users] force field for selinomethionine?

As far as I see others just replace selenium with sulphur, convert of selenomethionine to methionine like:https://bmccancer.biomedcentral.com/articles/10.1186/1471-2407-14-775 On Wednesday, November 1, 2017, 8:24:10 AM GMT+2, Seera Suryanarayana wrote: Dear

[gmx-users] force field for selinomethionine?

Dear gromacs users, I have to do simulations for a peptide which has the selinomethionine. But regular force fields from gromacs has no information for this residue. kindly give me information if is there any force field for selinometheoinine. Thanks in advance Surya Graduate student India. --

Re: [gmx-users] force field / parameters for NADH, FMN

On 10/30/17 10:58 AM, Hermann, Johannes wrote: Dear all, I want to simulate a complex consisting of a protein, FMN, and NADH. I have two problems/questions: 1) In the "CHARMM36 all-atom force field (March 2017)" parameters for NADH are present. But apparently I am using a wrong atom

[gmx-users] force field / parameters for NADH, FMN

Dear all, I want to simulate a complex consisting of a protein, FMN, and NADH. I have two problems/questions: 1) In the "CHARMM36 all-atom force field (March 2017)" parameters for NADH are present. But apparently I am using a wrong atom naming convention (I copied / pasted NADH from a pdb

[gmx-users] force field for acetylated protein pdb file

Hi! I acetylated K40 my heterodimer's PDB file using PyTMs in PyMOL. Now I need to simulate it using GROMACS. Which force field would be the best for this purpose? Thank you in advance! Regards, Raag -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Force field for Cobalt topology??

On 2/6/17 9:08 AM, Amir Zeb wrote: Hello gmx users, I'm wondering which would be the best force field to create topology for cobalt. I tried different ff but none of them get the task. I searched the mailing archive too but I couldn't get the way to solve the issue. Dr. Justin has just

[gmx-users] Force field for Cobalt topology??

Hello gmx users, I'm wondering which would be the best force field to create topology for cobalt. I tried different ff but none of them get the task. I searched the mailing archive too but I couldn't get the way to solve the issue. Dr. Justin has just mentioned (https://www.mail-archive.com/gmx

Re: [gmx-users] Force field for ion-carbon interaction

Thank you very much Alex :) On Thursday, December 22, 2016, Alex wrote: > Sorry to hear this. There is a good chance your reviewer is being an > obtuse donkey. As a fellow modeler and also a referee, I'd be much more > worried if someone _did not_ use a standard and

Re: [gmx-users] Force field for ion-carbon interaction

Sorry to hear this. There is a good chance your reviewer is being an obtuse donkey. As a fellow modeler and also a referee, I'd be much more worried if someone _did not_ use a standard and well-tested description for ions. Best of luck! :) Alex On 12/21/2016 11:40 PM, Maryam Kowsar wrote:

Re: [gmx-users] Force field for ion-carbon interaction

Hi Maryam, I am not really sure what "most proper" means when it comes to MD simulations, but I think if we're talking about vdw/electrostatics, AMBER and OPLS-AA are very close and have been used widely in the presence of things like CNTs and graphene... If there's any particular effect you are

[gmx-users] Force field for ion-carbon interaction

Dear all What is the best and most proper force field for ions (like Na+ and Ca2+) and carbon structured systems interactions? I found a few papers which used Amber force field. Has anyone worked with or seen any papers in this regard? Thanks. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Force field transformation from Gromacs to Charmm format

Thank you very much! How can I transform the gaff (general amber) force field files into Gromacs force field files? Do you have these tools? I want to transform *.lib generated by tleap to *.itp and *.top. -- With my best wishes, Ming Li, PhD Chinese Academy of Agricultural Sciences,

Re: [gmx-users] Force field transformation from Gromacs to Charmm format

Thank you! I will definitely have a close look at that. Best regards, Dawid 2016-12-19 2:33 GMT+01:00 Justin Lemkul : > > > On 12/18/16 12:22 PM, Dawid das wrote: > >> Dear All, >> >> Have you ever seen a script/tool that allows for transformation of the >> Gromacs force field

Re: [gmx-users] Force field transformation from Gromacs to Charmm format

On 12/18/16 12:22 PM, Dawid das wrote: Dear All, Have you ever seen a script/tool that allows for transformation of the Gromacs force field files into CHARMM force field files? I can see that there is a Pythons script that does the other way around. Also I could use a tool that creates *.psf

[gmx-users] Force field transformation from Gromacs to Charmm format

Dear All, Have you ever seen a script/tool that allows for transformation of the Gromacs force field files into CHARMM force field files? I can see that there is a Pythons script that does the other way around. Also I could use a tool that creates *.psf file from *.top file. I googled for that

Re: [gmx-users] Force field for phosphorylated residues

Hi, What atoms do you have in that residue, what's in the c.tdb and .rtp for GLN in force field and what did you choose for termini? Mark On Fri, Dec 9, 2016 at 4:05 PM Seera Suryanarayana wrote: > Dear gromacs users, > > I have one protein with phosphoserine and

[gmx-users] Force field for phosphorylated residues

Dear gromacs users, I have one protein with phosphoserine and phosphothreonine. I want to do simulation, but I do not know which force field I have to use. None of the force field from gromacs has the information of phospho residues. Then I tried with charm36, but did work. Kindly suggest me

[gmx-users] Force-Field for Ketals

Hi, I want to model a linear compound that has a ketal component. While building the OPLSAA topology (.itp) file for this molecule I ran into not having the C-C-C angle parameterized in -O-(CH3)2C-O-. I have spent some time looking for a different force field that may have this entire molecule,

Re: [gmx-users] Force Field for amino acid and peptide

Hi, On Fri, May 27, 2016 at 12:55 PM Alexander Alexander < alexanderwie...@gmail.com> wrote: > Thanks for your response. > > What does "being compatible" mean here, please? > That someone has done a bunch of work and presented results that show that sets of parameters reproduce physically

Re: [gmx-users] Force Field for amino acid and peptide

Thanks for your response. What does "being compatible" mean here, please? Actually, the FF of the surface (meanly \sigma and \epsilon in L-J) was harvested via a series of parametrization of some parameters with the quantum calculation of the same parameters. So, how can I find the most

Re: [gmx-users] Force Field for amino acid and peptide

On 5/25/16 11:05 AM, Alexander Alexander wrote: Dear Gromacs user, I am going to simulate the binding free energy of some amino acid to a metal surface in aqueous solution and also peptide adsorption behavior into this surface. I know the force field of the surface as well as the better type

[gmx-users] Force Field for amino acid and peptide

Dear Gromacs user, I am going to simulate the binding free energy of some amino acid to a metal surface in aqueous solution and also peptide adsorption behavior into this surface. I know the force field of the surface as well as the better type of water for such a work, but I do not know which

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Faulkner, Matthew <m.faulk...@liverpool.ac.uk> Sent: Friday, September 04, 2015 7:42 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

On 9/4/15 9:07 AM, Faulkner, Matthew wrote: Thank you Justin, Do you know a suitable force field to use for a topolgy from PRODRG? I am aware that the topology from PRODRG may now be of the best quality but I want to run a short MDS as proof of concept first to see if the events I am

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

On 9/4/15 7:42 AM, Faulkner, Matthew wrote: I am trying to find a suitable force field for using Bicarbonate in an aqueous environment in my MDS. I can't find anything where Bicarbonate has been used this way in gromacs in the literature, does anybody know of a reference for me or have advice

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

2015 14:11 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution On 9/4/15 9:07 AM, Faulkner, Matthew wrote: > Thank you Justin, > > Do you know a suitable force field to use for a topolgy from PRODRG? I am > aware that the t

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

:26 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force field selection for free Bicarbonate molecules insolution Matthew, Quick question, what are you trying to examine with the addition of bicarbonate? -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

. Regards, Matthew. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 04 September 2015 13:58 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

My group works with the bicarbonate and similar anions in the context of CO2 chemisorption. You must exercise serious caution to assign correct electrostatic potential at the surface of the anion and account for hydration/solvation effects within the force field derivation procedure. On Fri,

Re: [gmx-users] Force field parameterisation

The only thing you need is to transfer partial charges. This can be done using a copy-paste tool. The Amber FF is within gromacs distribution, so the needed bond lengths will be picked up implicitly after you specify bonded atoms, e.g. using x2top or by hand. On Sat, Aug 22, 2015 at 8:28 AM,

[gmx-users] Force field parameterisation

Hi all, I am trying to parameterise a new compound in Gromacs (theoretical compound - my experimental collaborators are still trying to purify and mass spec it) using the Amber 99sb force field. After asking about, I now know that in Amber I would take my QM structure run antechamber (or R.E.D

Re: [gmx-users] force field

let me modify my previous message: in the g_x2top command, not grompp :-) On Sun, Aug 9, 2015 at 8:14 PM, Maryam Kowsar maryam.kow...@gmail.com wrote: Hi Mohammad, Yes that's possible. You should just have the necessary files of your desired forcefield(.atp,.itp,...), and put them in a

Re: [gmx-users] force field

On 8/9/15 12:59 PM, mohammad r wrote: Thank you MaryamI want to use this force field in the first step of generating the topology file (pdb2gmx command in the force field shown after this command). Is it possible? and unfortunately I don't know how to find the necessary files of this force

Re: [gmx-users] force field

I did a similar task. You should know the parameters and convert your files format to gromacs format. A bit difficult but possible. On Sun, Aug 9, 2015 at 9:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/9/15 12:59 PM, mohammad r wrote: Thank you MaryamI want to use this force field in

[gmx-users] force field

Hi; I want to use ff14SB Amberprotein force field. But it isn't included in the gromacs force fields list.Is it possible to use this force field? How can I add it in?Thank you, Mohammad. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] force field

Hi Mohammad, Yes that's possible. You should just have the necessary files of your desired forcefield(.atp,.itp,...), and put them in a folder. in the grompp command just add -ff folder name. that's all! It will use your forcefield instead of the present forcefields in gromacs. Regards, -Maryam

Re: [gmx-users] force field

Thank you MaryamI want to use this force field in the first step of generating the topology file (pdb2gmx command in the force field shown after this command). Is it possible? and unfortunately I don't know how to find the necessary files of this force field. I searched a lot but I didn't

Re: [gmx-users] Force-field bias???

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of SAPNA BORAH sapnauser...@gmail.com Sent: Wednesday, August 05, 2015 10:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? Dear all

Re: [gmx-users] Force-field bias???

-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of SAPNA BORAH sapnauser...@gmail.com Sent: Wednesday, August 05, 2015 10:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? Dear all, Thank you for your answers which

[gmx-users] Force-field bias???

Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some support on this, however, I am not sure how

Re: [gmx-users] Force-field bias???

I believe, yes, it can. Dihedrals can make a big difference... On Wed, Aug 5, 2015 at 7:24 AM, SAPNA BORAH sapnauser...@gmail.com wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that

Re: [gmx-users] Force-field bias???

On 8/5/15 6:24 AM, SAPNA BORAH wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that unfolding of the protein may be different with a change in force fields applied? Literature has given some

Re: [gmx-users] Force-field bias???

jalem...@vt.edu Sent: Wednesday, August 05, 2015 7:31 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? On 8/5/15 6:24 AM, SAPNA BORAH wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e

Re: [gmx-users] Force-field bias???

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Wednesday, August 05, 2015 7:31 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? On 8/5/15 6:24 AM, SAPNA

Re: [gmx-users] Force-field bias???

...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of SAPNA BORAH sapnauser...@gmail.com Sent: Wednesday, August 05, 2015 10:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? Dear all, Thank you for your answers which definitely clears some of my

Re: [gmx-users] Force-field bias???

...@maillist.sys.kth.se on behalf of SAPNA BORAH sapnauser...@gmail.com Sent: Wednesday, August 05, 2015 10:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Force-field bias??? Dear all, Thank you for your answers which definitely clears some of my doubts. I am trying to unfold a lectin

[gmx-users] Force field parameterization for PAMAM dendrimers

Dear all, I want to perform MD simuations on PAMAM dendrimers, but unfortunately this molecule has not been defined in any of the GROMACS force fields. Therefore, I should parameterize the force field for my purpose. How should I do this procedure? (It is mentionable that I read the

Re: [gmx-users] Force field parameterization for PAMAM dendrimers

Dear Farideh, We have recently published an article on PAMAM dendrimers. We used oplsaa forcefield. You can access the paper at http://pubs.rsc.org/en/content/articlelanding/2015/sm/c5sm00854a. Hope it helps. Chandan On Mon, May 18, 2015 at 12:58 PM, faride badalkhani

Re: [gmx-users] force field problem....

On 4/16/15 7:12 AM, Kamalesh Roy wrote: Dear all, please suggest for the topology for oleic acid.. The information retreived after we run editconf... as a result atoms of the molecule becoming non bonded..in the box.. editconf doesn't add or remove bonds. What you see in VMD (or

Re: [gmx-users] force field problem....

Hi, Justin Thank you so much. I should be much more cautious in the future. there is another interesting thing. why doesn't it give the warning regarding mismatching between CLA and CL when I use MG in the pdb and topol file? I did not copy CN88. actually, I typed it. I got those 2 parameters

Re: [gmx-users] force field problem....

On 4/16/15 9:09 AM, Ming Tang wrote: Hi, Justin Thank you so much. I should be much more cautious in the future. there is another interesting thing. why doesn't it give the warning regarding mismatching between CLA and CL when I use MG in the pdb and topol file? There is no connection

Re: [gmx-users] force field problem....

On 4/16/15 3:41 PM, Kamalesh Roy wrote: Hi Justin Thank you, for the helpI have made topology from PRODRG server and then manually edited as required...but the column gromos type is unknown unlike other molecule in the ff.. Where do I get this? You'll have to tell us what the molecule

Re: [gmx-users] Force field choosing and parameterization

Hi, Leandro Thanks for your explanation and tips. It helped me a lot. Initially, I'll try to do the parameterization for the fluorophore and substrate using GAFF and Antechamber, and then combine it with the AMBER forcefield. After that, I'll apply this new forcefield to carry out the MD

[gmx-users] Force field choosing and parameterization

Hi, I'm new here and I barely have experience in GROMACS. I'm seeking some help to solve an issue. I want to run MD simulations of an enzyme that: 1 - Have a fluorescent probe attached next to the catalytic site; 2 - Have a polysaccharide (substrate) embedded in its catalytic site; One

[gmx-users] Force field choosing and parameterization

Hi, I'm new here and I barely have experience in GROMACS. I'm seeking some help to solve an issue. I want to run MD simulations of an enzyme that: 1 - Have a fluorescent probe attached next to the catalytic site; 2 - Have a polysaccharide (substrate) embedded in its catalytic site; One

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