Re: [gmx-users] Covariance analysis of X-ray ensemble

Hello. Check your topology file. You should have had a mistake in matching the atoms. Best regards. Lucio. El vie, 11-01-2013 a las 21:46 +0300, James Starlight escribió: > Tsjerk, thanks for suggestion! > > By the way I've found in the pca.log ( that time pca was done on > trajectory as well

Re: [gmx-users] losing data in trjconv?

Hello, you have to use the -force parameter in trjconv, to copy also the forces in the original trr file. Best regards Lucio El lun, 15-10-2012 a las 21:18 +0800, Gil Claudio escribió: > Hi Justin, > > My original intention was to lessen the 5 ns trajectory to transfer to > another drive. I did

Re: [gmx-users] In Silico Compound Library Search

The ZINC database page and the NIH PubChem one can help you in that. Best regards Lucio El sáb, 19-05-2012 a las 18:10 -0700, Nancy escribió: > Hi All, > > Does anyone know of a free cheminformatic service from which it's > possible to narrow down a search for molecules by inputting limits on > th

Re: [gmx-users] Residue 'FOR' not found in residue topology database

Hello. You have to check whether the formyl residue is defined with other name in the force field files. If not, you have to get the parameters for it. Best regards Lucio Montero El jue, 12-04-2012 a las 00:40 -0700, Shima Arasteh escribió: > Dear Gromacs friends, > > > I attached my .pdb file in

Re: [gmx-users] re: Acpype error

You should check also that you use for acpype a python installation under which the openbabel is installed. Lucio Montero Instituto de Biotecnología, UNAM. --- El mar, 12-04-2011 a las 07:29 -0700, Aldo Segura escribió: > First of all, I don't kn

Re: [gmx-users] Re: PRODRG server

-- > > > > > > > > -- > > > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > >

Re: [gmx-users] pdb file

I opened your file in the molecular viewer Chimera and it displayed all the bonds. Molecular viewers have different ways of estimated if atoms are bonded or not. Hope it helps. --- Lucio Montero PhD Student Insituto de Biotecnologia, UNAM, Mexico. El vie, 0

Re: [gmx-users] Energy minimization: problems with ramachanrad score

he homology models in a waterbox? After all > that the native conformation is in aqua solution. > -- Lucio Ricardo Montero Valenzuela Estudiante de doctorado en Ciencias Bioquímicas Lab. del Dr. Federico Sánchez Instituto de Biotecnologia, UNAM Depar

[gmx-users] LIE in reruning PME NPT runs

Hello, I have run a MD for a protein-ligand complex, using the NPT ensemble and PME. I know that one should not use LIE in a MD that uses PME, because of the long-range energy term. But, if I build a new tpr file using coulombtype = shift instead of PME, and I use mdout -rerun to generate new energ

Re: [gmx-users] Re: moleculetype CU1+ is redefined

Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] about PRODRG

Try specifying manually the hybridization of the heavy atoms and the protonation. Best regards. Lucio Montero. Laboratorio del Dr. Federico Sánchez Ext. 27666 Departamento de Biología Molecular de Plantas Instituto de Biotecnología, UNAM Cuernavaca, Morelos, 62210 El mar, 25-05-2010 a las 16:11 +0

Re: [gmx-users] Computational Alanine Scanning

When you re-generate hydrogens, you are introducing some extra disorder to the system. What I did is to write a script to rename the hydrogens. For example, there are residues that have the hydrogen numbering starting from 2 (eg. hydrogens on CB of lysine had hydrogens starting from HB2). In the sc

Re: [gmx-users] help

hello. I got the same error, because I was using an NPT ensemble to do a position-restrained simulation, and the error disappeared when I did the position-restrained simulation with NVT. Best regards. Lucio. El mar, 27-04-2010 a las 16:52 +0530, vani ms escribió: > hello > i got the warning as the

Re: [gmx-users] 'SHAKE' : gromacs 4.0.7

When you run GROMACS in parallel, by default it does domain descomposition, so if your constraints run across the charge groups, SHAKE can not run. El mar, 20-04-2010 a las 14:49 -0700, Ramachandran G escribió: > Hello gromacs users: > I installed the new version of gromacs and tried to ru

[gmx-users] GROMACS reproducibility

analysis?. Sincerely yours. Lucio. -- Lucio Ricardo Montero Valenzuela Estudiante de doctorado en Ciencias Bioquímicas Lab. del Dr. Federico Sánchez Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico

Re: [gmx-users] Potein-protein complex simulations

If you are working with a two-protein complex, you don't need PRODRG. You can create the complex topology in pdb2gmx using as input a PDB file with two chains, each chain for a protein. Then pdb2gmx does the job of creating an itp file for each protein, and a top file for the complex, which has #in

Re: [gmx-users] amber force field in Gromacs

This kind of problems can occur if you were restraining atom positions and using pressure coupling. Best regards Lucio. Lucio Ricardo Montero Valenzuela PhD Student Laboratorio del Dr. Federico Sánchez Ext. 27666 Departamento de Biología Molecular de Plantas Instituto de Biotecnología, UNAM

[gmx-users] Protonation and solvation software

What is the best software for protonating and for solvating pdb files for doing Molecular Dynamics with GROMACS?. Best regards. Lucio. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa

[gmx-users] Gromacs 3.3.1 with acpypi

Is there any problem for using the current version of acpypi for preparing topologies for using the version 3.3.1 of gromacs?. Best regards. Lucio. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pl

Re: [gmx-users] parameters for Phosphorylated threonine and serine

net > > Explorer 8 > > > <http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/>. > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry

Re: [gmx-users] simulation of protein in presence of ATP

Hi nikhil damle When running pdb2bmx for ATP in a PDB file using the ffG43a1, shows warnings because atom names don't match. You have to cut the ATP coordinates out to other PDB file, to convert it to gromacs format (.gro) using editconf and edit this file in gromacs format to match the atom naming

Re: [gmx-users] Alternative TRP residue

The acpypi program can calculate the topology files for your molecule. I have done it for non-polymeric molecules, but I don't know if there have to be extra work in polymeric molecules like amino acids. El jue, 11-06-2009 a las 17:09 +0200, abelius escribió: > Dear All, > > I have AmberFF paramet

Re: [gmx-users] Replacing the PRODRG charges

The target forcefield will be G43a1. But I would move to more recent versions of GROMOS 53a5 or 53a6. El jue, 04-06-2009 a las 16:29 +1000, Mark Abraham escribió: > Lucio Ricardo Montero Valenzuela wrote: > > I want to run a MD in an unparameterized molecule similar to adenine. I can

[gmx-users] Replacing the PRODRG charges

AMBER, GLYCAM and OPLS forcefields)?. Or will it be mixing forcefields?. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico

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

al/justin > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search befo

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

David van der Spoel : > 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? > >

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

g/mailman/listinfo/gmx-users > >> Please search the archive at http://www.gromacs.org/search before > >> posting! > >> Please don't post (un)subscribe requests to the list. Use the www > >> interface or send it to gmx-users-requ...@gromacs.org. > >>

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

lease don't post (un)subscribe requests to the list. Use the www > >> interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ___ > >

Re: [gmx-users] how to parametrize Phos. Thr TPO

> # IDIHS: 2893 > # LJ14: 9248 > > --- > Program grompp, VERSION 3.3.2 > Source code file: grompp.c, line: 1182 > > Fatal error: > There were 2 errors in input file(s) > --- >

[gmx-users] OPLS-AA topologies for ATP/ADP.

Does anybody have the topology files for ATP and/or ADP for the OPLS-AA forcefield?. If not, how can I parameterize this molecules?. Best regards. Lucio Montero. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad

Re: [gmx-users] SO3- force field

; >   > > > > > > > > > > > > > > > > > > > [ÇѸÞÀÏ Express]¸ÞÀϸñ·Ï°ú ¹Ì¸®º¸±â¸¦ µ¿½Ã¿¡! > > > > > > > > > > > > > > > Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departa