[gmx-users] forcefield and setting

 Dear Justin I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for water. em.mdp file: title   =  n.pdb cpp =  /lib/cpp define  =  -DFLEXIBLE constraints =  none integrator  =  steep nsteps  =  4 co

Re: [gmx-users] forcefield and setting

On 9/19/13 11:59 AM, fatemeh ramezani wrote: Dear Justin I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for water. em.mdp file: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator

Re: [gmx-users] Forcefield parameters for AcetylCoA

Please keep the discussion on the gmx-users mailing list. On 7/11/12 10:43 AM, panbazha wrote: Dear Justin, That file was generated by me in ATB, The issue is when i looked into the united atom itp file, I found many bonds and angles has not determined. So, just wondering if there are any publi

Re: [gmx-users] Forcefield parameters for AcetylCoA

On 7/11/12 8:18 AM, Padmanabhan Anbazhagan wrote: Dear All, Could anyone please suggest me some article or information that contains force field parameters (gromacs53A6) for acetyl Coenzyme A Google turned up: http://compbio.biosci.uq.edu.au/atb/download.py?molid=5470 -Justin -- =

[gmx-users] Forcefield parameters for AcetylCoA

Dear All, Could anyone please suggest me some article or information that contains force field parameters (gromacs53A6) for acetyl Coenzyme A Thanks in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are a

Re: [gmx-users] Forcefield question

On 13/02/2012 9:46 PM, Matthias Ernst wrote: Hi, I am currently working with the AMBER forcefields provided by GROMACS. I noticed there are atoms in the forcefields (e.g. amber99 or amber03) with LJ parameters of 0.0 for sigma and epsilon. For example, the HO atom type is sometimes used (e.g.

[gmx-users] Forcefield question

Hi, I am currently working with the AMBER forcefields provided by GROMACS. I noticed there are atoms in the forcefields (e.g. amber99 or amber03) with LJ parameters of 0.0 for sigma and epsilon. For example, the HO atom type is sometimes used (e.g. in SER or in the terminal Hs of DNA residues

Re: [gmx-users] Forcefield for Lipids

Saumya wrote: Hello all, I am trying to simulate the DMPC Lipid Bilayer with water molecules. I am using Charmm27 forcefield for that. I obtain the starting structure from Charmm-GUI. The pdb file that I obtain has "DMPC" as the residue name for the lipid molecules. I checked the "lipid.rtp

[gmx-users] Forcefield for Lipids

Hello all, I am trying to simulate the DMPC Lipid Bilayer with water molecules. I am using Charmm27 forcefield for that. I obtain the starting structure from Charmm-GUI. The pdb file that I obtain has "DMPC" as the residue name for the lipid molecules. I checked the "lipid.rtp" file in Charmm27 an

Re: [gmx-users] Forcefield parameters

rote: I think manual 5.3.3 covers the relevant points. Let me know what is not clear. Mark - Original Message - From: Sai Pooja mailto:saipo...@gmail.com>> Date: Wednesday, October 27, 2010 9:41 Subject: Re: [gmx-users] Forcefield parameters

Re: [gmx-users] Forcefield parameters

I think manual 5.3.3 covers the relevant points. Let me know what is not clear. Mark - Original Message - From: Sai Pooja Date: Wednesday, October 27, 2010 9:41 Subject: Re: [gmx-users] Forcefield parameters To: Discussion list for GROMACS users > > > On Tue, Oct 26, 201

Re: [gmx-users] Forcefield parameters

On Tue, Oct 26, 2010 at 6:04 PM, Mark Abraham wrote: > > > - Original Message - > From: Sai Pooja > Date: Wednesday, October 27, 2010 8:52 > Subject: Re: [gmx-users] Forcefield parameters > To: Discussion list for GROMACS users > > > On Tue, Oct 26, 201

Re: [gmx-users] Forcefield parameters

- Original Message - From: Sai Pooja Date: Wednesday, October 27, 2010 8:52 Subject: Re: [gmx-users] Forcefield parameters To: Discussion list for GROMACS users > On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul wrote: > > > Sai Pooja wrote: > > > On T

Re: [gmx-users] Forcefield parameters

Sai Pooja wrote: On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul > wrote: Sai Pooja wrote: On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrote:

Re: [gmx-users] Forcefield parameters

On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul wrote: > > > Sai Pooja wrote: > > >> >> On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Sai Pooja wrote: >> >>Hi, >> I want to change the non-bonded parameters to modify the >>int

Re: [gmx-users] Forcefield parameters

Sai Pooja wrote: On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul > wrote: Sai Pooja wrote: Hi, I want to change the non-bonded parameters to modify the interaction between water molecules and protein molecules. I am using CH

Re: [gmx-users] Forcefield parameters

On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul wrote: > > > Sai Pooja wrote: > >> Hi, >> I want to change the non-bonded parameters to modify the interaction >> between water molecules and protein molecules. >> I am using CHARMM forcefield with Tip3p water. >> The ffnonbonded.itp file of th

Re: [gmx-users] Forcefield parameters

Sai Pooja wrote: Hi, I want to change the non-bonded parameters to modify the interaction between water molecules and protein molecules. I am using CHARMM forcefield with Tip3p water. The ffnonbonded.itp file of the forcefield has non-bonded parameters for tip3p water. Can I achieve the

[gmx-users] Forcefield parameters

Hi, I want to change the non-bonded parameters to modify the interaction between water molecules and protein molecules. I am using CHARMM forcefield with Tip3p water. The ffnonbonded.itp file of the forcefield has non-bonded parameters for tip3p water. Can I achieve the above by changing these p

Re: [gmx-users] forcefield

Hi Lalitha, Zebularine is beyond the trivial. You may be able to derive something reasonable from the other bases using 'chemical intuition' (cytidine, thymidine, uracil), but it's likely that the electronic structure of the ring is too different to justify an approach like that. Likely you should

[gmx-users] forcefield

Hi, I want to do simulation with the ligand called zebularine. I dont find forcefied for that. Also i read prodgr has been deprecated.. Could you please help me to find out the forcefield for the ligand zebularine. Thanks in advance lalitha __

Re: [gmx-users] forcefield for free (neutral) amino acids

FyD wrote: Dear chun feng, I am not a user of GROMACS, but I hope someone who's working on protein dynamics can do me a favor here. I am desperately searching for a forcefield for free and neutral amino acids. But it seems that the forcefields such as amber and opls only parametrizes amino

Re: [gmx-users] forcefield for free (neutral) amino acids

Dear chun feng, I am not a user of GROMACS, but I hope someone who's working on protein dynamics can do me a favor here. I am desperately searching for a forcefield for free and neutral amino acids. But it seems that the forcefields such as amber and opls only parametrizes amino acids

[gmx-users] forcefield for free (neutral) amino acids

Hi all: I am not a user of GROMACS, but I hope someone who's working on protein dynamics can do me a favor here. I am desperately searching for a forcefield for free and neutral amino acids. But it seems that the forcefields such as amber and opls only parametrizes amino acids in peptides (with

Re: [gmx-users] Forcefield to choose

vivek sharma wrote: Hi everybody, I am running MDS for protein molecule using GROMACS, but I am not sure of which forcefield I should use. Can anybody suggest me the criteria for choosing forcefield ? Every force field has its inherent benefits and limitations. There is no substitute for

[gmx-users] Forcefield to choose

Hi everybody, I am running MDS for protein molecule using GROMACS, but I am not sure of which forcefield I should use. Can anybody suggest me the criteria for choosing forcefield ? Also, I am using drug-enzyme tutorial by John E. Kerrigan titled "GROMACS Tutorial for Drug – Enzyme Complex." where

Re: [gmx-users] forcefield validation

> > First, thanks very much for your instruction. If quantum chemical > calculation does not have any physical meaning, how should I decide the > partial charge for a molecule? David is correct, he was referring to Mulliken charges. Again, there is no *right* answer to this, the name of the game

Re: [gmx-users] forcefield validation

Hi, Many > articles didn't give out the validation procedure of their topologies in > detail, are there some classic articles explaining how the forcefield we > used today, such as OPLS, GROMOS, AMBER and CHARMM , developed? I want to > know how they were deduced from the very beginning. There

Re: [gmx-users] forcefield validation

Qin Shanshan wrote: > > First, thanks very much for your instruction. If quantum chemical > calculation does not have any physical meaning, how should I decide the > partial charge for a molecule? > I think Mark referred to Mulliken charges. Check how your favorite FF does it and follow the re

[gmx-users] forcefield validation

First, thanks very much for your instruction. If quantum chemical calculation does not have any physical meaning, how should I decide the partial charge for a molecule? Any suggestion will be appreciated, thanks very much in advance.___ gmx-users maili

Re: [gmx-users] forcefield validation

Qin Shanshan wrote: > Thanks very much for your patient explaination.It really is a question > confusing me much. What I am interested in is inserting some organic > molecules into lipid bilayers. Tieleman's lipid parameters have given > out the interactive LJ parameters with ffgmx forcefield. S

[gmx-users] forcefield validation

Thanks very much for your patient explaination.It really is a question confusing me much. What I am interested in is inserting some organic molecules into lipid bilayers. Tieleman's lipid parameters have given out the interactive LJ parameters with ffgmx forcefield. So if I want to simulate lipi

[gmx-users] forcefield validation

Thanks very much for your patient explaination.It really is a question confusing me much. What I am interested in is inserting some organic molecules into lipid bilayers. Tieleman's lipid parameters have given out the interactive LJ parameters with ffgmx forcefield. So if I want to simulate lipi

Re: [gmx-users] forcefield validation

Alan Dodd's suggestion is nice, but there isn't always a lot of experimental data available for a particular molecule we can compare with -- or perhaps we want to begin with "good" parameters and then see if our method can reproduce experiment. Anyway, for whatever reason it isn't always possible t

Re: [gmx-users] forcefield validation

done. - Original Message From: Qin Shanshan <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, October 16, 2007 2:48:44 PM Subject: [gmx-users] forcefield validation Dear gms-users, I have a fundamental question to put forward. If I want to construct a forcefield for

[gmx-users] forcefield validation

Dear gms-users, I have a fundamental question to put forward. If I want to construct a forcefield for an organic molecule of middle size,which has about 100 atoms, how can I prove that my forcefield for this molecule is correct? Althouth we can get ffgmx itp files from prodrg server, can we be s

Re: [gmx-users] forcefield problems - advice needed

> hi guys, > > for quite a long time i am trying to 'create' a forcefield for aliphatic > alcohols (right now, for ethanol) to use with a water potential we > employ in our simulations. > > there is a problem - the water potential uses combination rule 2, so i > thought i would just try to use FFGM

[gmx-users] forcefield problems - advice needed

hi guys, for quite a long time i am trying to 'create' a forcefield for aliphatic alcohols (right now, for ethanol) to use with a water potential we employ in our simulations. there is a problem - the water potential uses combination rule 2, so i thought i would just try to use FFGMX and OPL

[gmx-users] Forcefield parameters for Cobalt in gromacs-3.3.1?

Hi, I was wondering if anyone has used Cobalt(3+) in their work. I am trying to find the forcefield parameters of cobalt hexamine [Co(NH3)6]+++ Thanks, Narayan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

[gmx-users] ForceField for SDPC(sphingomyelin)

Dear Gmx community I am new to memberane simulation. i want to simulate membrane, which consists DPPC and SDPC(Sphingomyelin). luckily, i got the force field and coordinates for DPPC (dppc.itp,dppc.pdb) from Doctor Peter Tieleman'websites.however,i cannot find the force field and coordinates for

Re: [gmx-users] forcefield

Dear Hadi, You also forgot to define "better". What do you want to learn from that peptide? Do you need all hydrogens for that? Or could you do without? Also consider that the generality of the question phrased does usually not trigger people in a way desired for reply. It sounds a bit like "I've

Re: [gmx-users] forcefield

hadi behzadi wrote: Hi all of users For HHAHHAADAAHHAAD peptide what kinde of force field is better ? I don't know, but I could tell you the answer immediately for HHAHAHADAAHHAAD peptide :-P General force fields are parameterized to be reasonable over a range of systems. The overview of

[gmx-users] forcefield

Hi all of users   For HHAHHAADAAHHAAD peptide what kinde of force field is better ?     New Yahoo! Messenger with Voice. Call regular phones from your PC and save big.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman