[gmx-users] force field parameter for ligands

Dear all, where do you usually get topolgy for small molecule ligand or do it manually? Dundee PRODRG Server seems to be capable of making .top for ffgmx only but not new ones like ffG53a6,etc. Thanks Johnny ___ gmx-users mailing listgmx-users@g

[gmx-users] oplsaa parametrization

Dear Users I m trying to simulate a structure (not a protein) which is not parametrized in oplsaa FF. I created the structure using PRODRG and included the results of *.itp from PRODRG to ffoplsaa.rtp file and tried to use available oplss_xxx for my atom type near to those ones already exists in *.

Re: [gmx-users] oplsaa parametrization

R. A. wrote: > Dear Users > I m trying to simulate a structure (not a protein) which is not > parametrized in oplsaa FF. I created the structure using PRODRG and > included the results of *.itp from PRODRG to ffoplsaa.rtp file and > tried to use available oplss_xxx for my atom type near to those on

[gmx-users] Re: force field parameter for ligands

> >Message: 1 >Date: Mon, 25 May 2009 01:15:44 -0700 >From: "Zhanglin Ni" >Subject: [gmx-users] force field parameter for ligands >To: >Message-ID: <009701c9dd11$012c1ae0$0301a...@zn3> >Content-Type: text/plain; format=flowed; charset="iso-8859-1"; > reply-type=original > >Dear all, >where

Re: [gmx-users] oplsaa parametrization

Dear Ran Thanks for the reply. I think I `ve read some papers using PRODRG and opls. However they didnt mention clearly that how they parametrized their force field. Just do you know any alternative software. As I checked many softwares but I couldnt find any to create .itp file at the same time.

Re: [gmx-users] oplsaa parametrization

Hi Rosa, You can read the paper on PRODRG to study how they parametrise. There's a topology builder for OPLS-AA: http://labmm.iq.ufrj.br/mktop/ There're also commercial tools (see some previous posts on the mailing list) and you can also start with PRODRG and modify the files to have the right pa

Re: [gmx-users] force field parameter for ligands

Zhanglin Ni wrote: Dear all, where do you usually get topolgy for small molecule ligand or do it manually? Dundee PRODRG Server seems to be capable of making .top for ffgmx only but not new ones like ffG53a6,etc. Thanks Search. There's a million posts on this mailing list pointing out that t

[gmx-users] some puzzled about the dihedral paramaters

gmx-users， Dear all, I make a *.itp for benzene by myself. All parameters come from the ffoplsaabon.itp and ffoplsaanb.itp. while I have some puzzled about the dihedral parameters of benzene. In ffoplsaabon.itp file, there are dihedral parameters of benzene and the potential function is 3, lik

Re: [gmx-users] some puzzled about the dihedral paramaters

Jinyao Wang wrote: > gmx-users， > Dear all, > > I make a *.itp for benzene by myself. All parameters come from the > ffoplsaabon.itp and ffoplsaanb.itp. while I have some puzzled about the > dihedral parameters of benzene. You should check out the literature of OPLS/AA and see how aromatic rin

[gmx-users] Lingering problems with the test set

Hi All, I just grabbed the latest version of the test set from CVS, noting the updates and improvements to the package. I ran gmxtest.pl, and all simple, complex, and kernel tests passed, but pdb2gmx failed. Looking into the pdb2gmx.log file, grompp complains about "Unknown or double left-h

[gmx-users] maximum size for Freeze group?

Hi, I built an Argon box around my system that shall work as walls. Therefore all Argon atoms should be frozen. There are 33900 Argon atoms in my system but during grompp-ing the following message occurs: Making dummy/rest group for T-Coupling containing 62956 elements Making dummy/rest gr

Re: [gmx-users] Why NaCl and KCl solution?

The crystalization chemical conditions should appear described in the header of your PDB file, there you can see if there were, for example, sodium ions. Lucio Montero PhD. Candidate Instituto de Biotecnologia, UNAM Mexico Mensaje citado por "Justin A. Lemkul" : > > Chih-Ying Lin wrote: > > HI

[gmx-users] Viscosity using periodic perturbation method

Dear users: I was trying to calculate the viscosity of liquid system using periodic perturbation method. Does this method require NVT ensemble simulation in stead of NPT ? Because I read some literature on periodic perturbation method. they all used NVT. I did not found any information about this

[gmx-users] amber to gromos topology

Hi all, there is a tool to convert an amber topology to a gromos one? byegiordano ---Valore legale alle tue mailInterfreePEC - la tua Posta Elettronica Certificatahttp://pec.interfree.it---

Re: [gmx-users] amber to gromos topology

baloilgiull...@interfree.it wrote: Hi all, there is a tool to convert an amber topology to a gromos one? There is no straightforward (or inherently appropriate) way to convert AMBER parameters to GROMOS parameters. If you want to convert an AMBER-formatted topology to one suited for us

Re: [gmx-users] oplsaa parametrization

Dear Ran Thank you so much for the suggestion and comments. I ll check it out. Regards Rosa -- Be Yourself @ mail.com! Choose From 200+ Email Addresses Get a Free Account at www.mail.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.

[gmx-users] Dynamics with DNA

Hi folks ! Does someone knows how to perform Molecular dynamics simulations of DNA molecules using GROMACS 3.3.2 ? Is that possible ? With forcefield should I use ? If it is not possible with GROMACS does someone have a suggstions of which software colud be used ? Best whises, Tano

Re: [gmx-users] maximum size for Freeze group?

ilona.bal...@bioquant.uni-heidelberg.de wrote: Hi, I built an Argon box around my system that shall work as walls. Therefore all Argon atoms should be frozen. There are 33900 Argon atoms in my system but during grompp-ing the following message occurs: Making dummy/rest group for T-Coupling

Re: [gmx-users] Dynamics with DNA

ta...@ime.eb.br wrote: Hi folks ! Does someone knows how to perform Molecular dynamics simulations of DNA molecules using GROMACS 3.3.2 ? Is that possible ? With forcefield should I use ? If it is not possible with GROMACS does someone have a suggstions of which software colud be used ?

Re: [gmx-users] Dynamics with DNA

ta...@ime.eb.br wrote: Hi folks ! Does someone knows how to perform Molecular dynamics simulations of DNA molecules using GROMACS 3.3.2 ? Is that possible ? With forcefield should I use ? If it is not possible with GROMACS does someone have a suggstions of which software colud be used ?

Re: [gmx-users] Lingering problems with the test set

Justin A. Lemkul wrote: Hi All, I just grabbed the latest version of the test set from CVS, noting the updates and improvements to the package. I ran gmxtest.pl, and all Actually there were a bunch more improvements that I'd made which hadn't been correctly added to CVS. Erik's fixed that

Re: [gmx-users] Dynamics with DNA

> Nearly all the force fields that can be used with Gromacs have > nucleic acids represented as fundamental building blocks. That may be true, but does not mean that in all these force fields the parameters are good enough to assess 'real' behaviour of nucleic acids. E.g. the older GROMOS force fi