Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Hi, Thanks for answering and sorry to take so long to reply. After your response I went seach for more information about that. What I read here in the list is that some people uses antechamber to generate am1-bcc charges (or RESP charges using Gaussian program) and convert the output

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

example: http://wiki.gromacs.org/index.php/Parameterization -Justin Regards, Josmar Rocha --- Em *sex, 27/3/09, Ran Friedman, Biochemisches Inst. //* escreveu: De: Ran Friedman, Biochemisches Inst. Assunto: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigne

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

parameter derivation. See, for example: http://wiki.gromacs.org/index.php/Parameterization -Justin Regards, Josmar Rocha --- Em *sex, 27/3/09, Ran Friedman, Biochemisches Inst. //* escreveu: De: Ran Friedman, Biochemisches Inst. Assunto: Re: [gmx-users] HF/6-31G** ESP derived

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Friedman, Biochemisches Inst. escreveu: De: Ran Friedman, Biochemisches Inst. Assunto: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones Para: bije...@yahoo.com.br, "Discussion list for GROMACS users" Data: Sexta-feira, 27 de Março de 2009, 17:35 Dear Jo

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

I wanted the OPLS-UA because my system is large (3 proteins with 2 organic molecules, in water), and, if the G43a1 forcefield gives me a MD speed of 70 ps/day, an all atom model will result much slower. So what else can I do to speed up my MD, to get results in 1-3 months?. Mensaje citado por David

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Hi, I've recently used OPLS-AA for a similar calculation. It has the advantage that many atom types are already defined in Gromacs and that QM-based calculations give you reasonable charges. Note that it may take considerable simulation time (tens of ns) to discriminate between similar docke

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Lucio Ricardo Montero Valenzuela wrote: So it 's better to switch to the OPLS forcefield if I want to compute the charges?. How can I implement the OPLS-UA if my gromacs (version 3.3) only includes the OPLS-AA? We don't support United atom OPLS because Jorgensen himself does not use it anymore

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

So it 's better to switch to the OPLS forcefield if I want to compute the charges?. How can I implement the OPLS-UA if my gromacs (version 3.3) only includes the OPLS-AA? Mensaje citado por "Justin A. Lemkul" : > > > Lucio Montero wrote: > > How about MOPAC to calculate the charges for 3-methylade

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

I have done the docking with autodock, and I want to do a MD satrting from the docked position. Mensaje citado por "Justin A. Lemkul" : > > > Lucio Montero wrote: > > How can you test the "ligands" when you don't know if they REALLY bind > > to the protein? > > > > Sounds like a job for docking an

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Lucio Montero wrote: How about MOPAC to calculate the charges for 3-methyladenine (this molecule has a charge +1) for using the G43a1 force field?. That may not be a bad place to start, but any parameters applied to a Gromos molecule have to reproduce condensed phase thermodynamic observa

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Lucio Montero wrote: How can you test the "ligands" when you don't know if they REALLY bind to the protein? Sounds like a job for docking and/or binding energy calculations. -Justin -- From: "Ran Friedman, Biochemisches Inst." Sent: Friday

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

How can you test the "ligands" when you don't know if they REALLY bind to the protein? -- From: "Ran Friedman, Biochemisches Inst." Sent: Friday, March 27, 2009 2:35 PM To: ; "Discussion list for GROMACS users" Subject: Re: [gmx-users] HF/6-31G

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

How about MOPAC to calculate the charges for 3-methyladenine (this molecule has a charge +1) for using the G43a1 force field?. -- From: "Ran Friedman, Biochemisches Inst." Sent: Friday, March 27, 2009 2:35 PM To: ; "Discussion list for GROMACS us

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with th

[gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-arc