[gmx-users] PubChem Online Compound Search and Download

y info about it. Thanks, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www

[gmx-users] In Silico Compound Library Search

ks in advance, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface

[gmx-users] Chelation of Calcium with Citrate

re the stoichiometric coefficients) Thanks in advance, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requ

[gmx-users] t-Butyl sulfinamide Stability

Hello, Does anyone know how stable sulfinamides are in vivo? Specifically, molecules such as Ellman's t-butyl sulfinamide. How does their stability compare to sulfoxides? Do they get oxidized in vivo? Are they at least stable in water? Thanks in advance, Nancy -- gmx-users mailing list

[gmx-users] Methanesulfinamide Stability and Synthesis

Hello All, I would greatly appreciate it if anyone has information on the stability of methanesulfinamide (SMILES: C[S](=O)N([H])[H]), as well as it's stability in water. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sear

[gmx-users] Dimethyl Sulfoxide EM Absorbance

Hi All, I would greatly appreciate it if anyone could provide a reference or information on the electromagnetic absorbance characteristics of dimethyl sulfoxide, especially in the region of 800-1400nm. Thank you, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] Dimethyl Sulfoxide Electromagnetic Absorbance

11:20 PM, David van der Spoel wrote: > On 2012-03-21 03:06, Nancy wrote: > >> Hi All, >> >> I would greatly appreciate it if anyone could provide a reference or >> information on the electromagnetic absorbance characteristics of >> dimethyl sulfoxide, especially

[gmx-users] Dimethyl Sulfoxide Electromagnetic Absorbance

Hi All, I would greatly appreciate it if anyone could provide a reference or information on the electromagnetic absorbance characteristics of dimethyl sulfoxide, especially in the region of 800-1400nm. Thank you, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Ice Surface Binding Simulations

Hi All, I would like to determine the ability of several small molecules and peptides to "bind" to an ice surface, using Gromacs. What would be the best procedure for doing so? Also, would topolbuild be a good choice for generating the topologies? Thanks in advance, Nancy -- gmx-use

Re: [gmx-users] Ice Crystal Structure

Thank you very much for the information. Nancy On 11/29/11, Dallas Warren wrote: > http://www.google.com.au/search?q=ice+crystal+coordinate+file&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en-US:official&client=firefox-a > > Second listed item contains (or leads you to

[gmx-users] Ice Crystal Structure

Hi All, I would like to perform molecular dynamics with an ice crystal surface; does anyone know if such a structure file can be obtained online? Thanks, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] RMSD Calculation

Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. Thank you very much, Nancy -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Best Program for Simulating Lipid Bilayers in Water

Hi All, I heard that LAMMPS is supposedly good for simulating lipid bilayers in water. I haven't used LAMMPS before; does anyone know if it would be worth to try it in addition to Gromacs? Thanks in advance, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

Re: [gmx-users] Automated RMSD Calculations

Thanks alot for the info. Nancy On Fri, Mar 25, 2011 at 6:22 PM, Justin A. Lemkul wrote: > > > Nancy wrote: > >> Hi All, >> >> I would like to calculate RMSDs of a large number of small molecule >> conformations against a reference conformation, is there a

[gmx-users] Automated RMSD Calculations

Hi All, I would like to calculate RMSDs of a large number of small molecule conformations against a reference conformation, is there a simple software program or method that can be used to perform such calculations? Thanks in advance, Nancy -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Gromacs on other Operating Systems

Thanks, I appreciate the clarification. Also, can Gromacs be accelerated with a laptop nVidia GPU (320M)? Nancy On Mon, Mar 21, 2011 at 9:09 PM, Justin A. Lemkul wrote: > > > Nancy wrote: > >> Hi All, >> >> I've used used Gromacs under Linux, and I&#x

[gmx-users] Gromacs on other Operating Systems

Hi All, I've used used Gromacs under Linux, and I'm wondering whether it can be used under Windows 7 and/or Snow Leopard (10.6.6). Thanks in advance, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archiv

[gmx-users] TZD Tautomer Distribution

Hi All, For pioglitazone, are the two tautomers depicted in the attached figure the major forms at pH 7.0? Also, are there any published articles, or other evidence that would confirm that this is indeed the correct tautomeric distribution at pH 7? Thank you, Nancy <>-- gmx-users mailin

[gmx-users] TZD Tautomers

ligand-protein interactions. Does anyone know if the diketone or enol, or perhaps a different tautomer, would be predominant at pH 7.4? Thanks in advance. Nancy <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] Tautomer Prediction

ot;Figure_2.gif". The different tautomeric forms predicted by MarvinSketch are shown in "Figure_3.gif". Can anyone explain where these predictions come from, and if they are correct? Thanks, Nancy <><><>-- gmx-users mailing listgmx-users@gromacs.org http://lis

[gmx-users] Pioglitazone Tautomers

of them. Which tautomer would be dominant at the physiological pH of ~7.0? Also, are there any software programs that can predict which tautomer would be correct? Thanks in advance, Nancy <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] Thiazolidinedione Tautomers

Hi All, In the figure illustrating the various tautomers, some are actually aromatic; wouldn't these be the predominant species at pH 7.4? Also, how could one start docking without a properly defined ligand? Thanks in advance, Nancy On Sun, Jan 2, 2011 at 8:30 PM, Mark Abraham wrote: &

[gmx-users] Thiazolidinedione Tautomers

, 21 30–33, as a reference, but it does make it clear as to which tautomer is most appropriate for simulating binding to a receptor protein at pH 7.4. Thanks in advance, Nancy <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please se

Re: [gmx-users] Adding Partial Charges for Small Molecules

Hi Justin, Thanks for the useful info. Nancy On Sun, Jun 13, 2010 at 8:54 PM, Justin A. Lemkul wrote: > > > Nancy wrote: > >> Hi All, >> >> I am trying to add partial charges to nicotinamide adenine dinucleotide >> (NAD+), for input to molecular simu

[gmx-users] Adding Partial Charges for Small Molecules

Gasteiger charges) is written below (and attached as NAD.mol2 with corresponding PNG structure image). Thanks in advance, Nancy @MOLECULE NAD.mol2 70741 0 0 SMALL USER_CHARGES @ATOM 1 C1

[gmx-users] Converting SDF to Mol2 Format

convert individual files using this method. Is there another way to convert a large number of SDF files to Mol2 format at once, and also preserve the filenames? Thanks in advance, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Ligand Binding to Homodimeric Proteins

the X-Ray crystal structure, as one would expect identical binding to both sides? Thank you very much. Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don&#

[gmx-users] Analyzing Protein-Ligand Interactions

input, determine protein-ligand interactions, list them, and visualize docked conformations? If anyone has information, I would greatly appreciate it. Thanks in advance, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] Fatal Error: Segmentation Fault

is problem. Thanks, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/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] Segmentation Fault Problem

and I am just using Mesa drivers (and it gives the same libGL warning). I am not sure where the "Segmentation Fault" comes from (or what it means in this case). Please advise, Thanks, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listin

[gmx-users] Saving PDB with Ligand from Docking

Hello, I ran a docking simulation, and I have results in .mol format, and a protein (.pdb format). I would like to save both as a single PDB file, as input for Gromacs. Please advise as to what is the best way to do this. Thanks, Nancy ___ gmx-users

Re: [gmx-users] Fatal Equilibration Errors

I'm glad to be of help; yes, I would like to beta test topolbuild 1.3. Thank you. On Thu, Aug 13, 2009 at 7:42 AM, Bruce D. Ray wrote: > On Wednesday, August 12, 2009 at 8:47:33 PM, Nancy > wrote: > > > In an earlier message, it was stated that topolbuild generated topo

Re: [gmx-users] Fatal Equilibration Errors

s the OPLS-AA force field used? Thank you. Nancy On Mon, Aug 10, 2009 at 6:22 PM, Bruce D. Ray wrote: > On Sunday, August 9, 2009 at 4:32:19 PM, Nancy > wrote: > > > I obtained the ethylene glycol (1,2-ethanediol) structure from the URL: > > http://www.rcsb.org

Re: [gmx-users] Fatal Equilibration Errors

Thank you for the article. Nancy On Mon, Aug 10, 2009 at 9:34 PM, Dallas B. Warren < dallas.war...@pharm.monash.edu.au> wrote: > You might want to consider the parameters I developed for propylene > glycol http://dx.doi.org/10.1021/mp8001667 ... might provide some > guid

Re: [gmx-users] Force Field Charge Parameters

2 (34), pp 10732–10740 Are you suggesting that the authors used incorrect parameters? On Mon, Aug 10, 2009 at 6:05 PM, Justin A. Lemkul wrote: > > > Nancy wrote: > >> Hello, >> >> I have successfully minimised and equilibrated two systems, one consisting >>

[gmx-users] Force Field Charge Parameters

are there programs that will automatically generate charge values and other parameters for an arbitrary molecule? Thank you. Nancy ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Fatal Equilibration Errors

picosecond. It remained in the trans conformation for the rest of the equilibration. Thanks, Nancy On Sun, Aug 9, 2009 at 5:49 PM, Nagy, Peter I. wrote: > > Dear Nancy, > > It was useful to find charges for the solute... I am not a GROMACS user, > so I do not know what checks

Re: [gmx-users] Fatal Equilibration Errors

Therefore, the hydrogen bonds do form, given the charges adopted from the methanol topology (O: -0.574, H: +0.398, CH2: +0.176). Do these charge values seem reasonable? The ethylene glycol lacks explicit non-polar hydrogens; is that normal for this type of system, force field

Re: [gmx-users] Fatal Equilibration Errors

) forms to the solvent molecules. Is this normal for such a system? Thank you. Nancy ==em.mdp== constraints = none integrator = steep nsteps = 1 emtol = 10.0 emstep = 0.01 nstlist = 2 c

Re: [gmx-users] Fatal Equilibration Errors

molecules; what type of thermostat is reasonable for such a system? Nancy On Sat, Aug 8, 2009 at 3:49 PM, Justin A. Lemkul wrote: > > > Nancy wrote: > >> Hello, >> >> I have successfully minimised and equilibrated ethylene glycol in a water >> box. I have notic

[gmx-users] Fatal Equilibration Errors

settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates There were 12 inconsistent shifts. Check your topology Segmentation fault === I don't know what is happening wrong. Plea

Re: [gmx-users] Energy Minimisation and Equilibration Problems

w what the problem might be? Thanks, Nancy On Thu, Aug 6, 2009 at 6:48 PM, Bruce D. Ray wrote: > On Thursday, August 6, 2009 at 4:08:18 PM, Nancy > wrote: > > > I have attempted to perform energy minimisation from scratch again, and > these are the > > com

Re: [gmx-users] Very High Forces During Minimisation

ering why the Lysozyme tutorial at: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html does not have the same problems? Is there a way to stop minimisation and continue later from that same point? Thanks, Nancy On Thu, Aug 6, 2009 at 6:45 PM, Justin A.

[gmx-users] Very High Forces During Minimisation

=== I believe that equilibration is failing because of the large forces on the molecules during minimisation (although I am not sure, as I was able to run a simulation without proper minimisation before). If at all possible, please advise on how to reduce the energies and forces during minimisati

Re: [gmx-users] Energy Minimisation and Equilibration Problems

mx, I noticed that most of the motion of the water molecules occurs within the first 50 picoseconds. Please advise on how to further minimise this system. Thank you. Nancy On Thu, Aug 6, 2009 at 2:23 PM, Bruce D. Ray wrote: > On Thursday, August 6, 2009 at 11:58:20 AM, Nancy > wrote

Re: [gmx-users] Energy Minimisation and Equilibration Problems

e what values of the energies are reasonable for this system, and how to minimise it further. Please advise. Thank you. Nancy On Thu, Aug 6, 2009 at 8:38 AM, Bruce D. Ray wrote: > On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy > wrote: > > I am trying to run equilibratio

[gmx-users] Energy Minimisation and Equilibration Problems

= yes gen_temp= 300 gen_seed= -1 == the system "blows up". Addtionally, the structure of the solute is incorrect (all atoms are bonded to each other). Please advise on how to minimise such a system further, and as to why the equilibration is so unsta

Re: [gmx-users] Energy Minimisation Values

rce = 2.1965221e+04 on atom 39 Norm of force = 2.1487129e+03 == Please advise on how to further decrease the forces. Thanks, Nancy On Wed, Aug 5, 2009 at 6:08 PM, Justin A. Lemkul wrote: > > > Nancy wrote: > >> Hello, >

[gmx-users] Energy Minimisation Values

what value of emtol is reasonable for this type of small system. Please advise Thanks Nancy ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/s

Re: [gmx-users] Re: MD Simulation Errors for Ethylene Glycol-Water System

ure of the ethanediol solute seems to be incorrect throughout the equilbration. I am unsure what is going wrong, please help. Thank you. Nancy On Wed, Aug 5, 2009 at 9:13 AM, Bruce D. Ray wrote: > On Tuesday, August 4, 2009, at 6:30:57 PM, Nancy > wrote: > > I am trying to simul

[gmx-users] MD Simulation Errors for Ethylene Glycol-Water System

20.6156 0.5033 0.1435 === I am not sure where the errors are occuring (I am also wondering if the absence of explicit non-polar hydrogens in the .gro files are relevant). Please adivse. Thanks. Nancy ___ gmx-users maili

Re: [gmx-users] Carbohydrate MD Simulation

I used gzip to uncompress the file first: # gzip -d topolbuild1_2_1.tgz and then I used tar: # tar -xvf topolbuild1_2_1.tar This seems to work. On Sat, Aug 1, 2009 at 6:05 PM, Justin A. Lemkul wrote: > > > Nancy wrote: > >> Hello, >> >> I downloaded &quo

[gmx-users] topolbuild1_2_1.tgz decompressing problem

se. Thank you. Nancy ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/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 lis

Re: [gmx-users] Carbohydrate MD Simulation

se. Thank you. Nancy On Sat, Aug 1, 2009 at 11:31 AM, Bruce D. Ray wrote: > On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy wrote: > > If it necessary to manually create force field parameters for each > molecule, then how can one run a > > simulation involving a number of arbitr

Re: [gmx-users] Carbohydrate MD Simulation

High-throughput "in silico" screening (e.g. for ligand-protein binding) has been performed on a number of systems. How are such automated simulations performed (I assume they utilize molecular dynamics)? On Fri, Jul 31, 2009 at 5:47 PM, Justin A. Lemkul wrote: > > > Nanc

Re: [gmx-users] Carbohydrate MD Simulation

capable of running simulations on arbitrary molecules without having to "piece together" a force field for each molecule? Thanks, Nancy On Fri, Jul 31, 2009 at 4:53 PM, Justin A. Lemkul wrote: > > > Nancy wrote: > >> Hello, >> >> I am trying to r

[gmx-users] Carbohydrate MD Simulation

--- Please help. Thank you, Nancy ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don&#

Re: [gmx-users] Viewing Trajectories with VMD

Thanks, it works. Nancy On Thu, Jul 30, 2009 at 7:12 PM, Joshua Adelman wrote: > Hi Nancy, > Is it loading it in, but not displaying it? If that's the case, you need to > load a pdb file in first or else VMD can't guess how to display the molecule > from position da

[gmx-users] Viewing Trajectories with VMD

Hello, I have generated several trajectory files (*.trr, *.xtc) from running MD simulations, and I can view them with the "ngmx" program included with GROMACS, but I am unable to view them in Visual Molecular Dynamics (VMD). Please advise. Than

Re: [gmx-users] How to Run Energy Minimisation

tep, but I do not know specifically what parameters to run the energy minimisation. Please advise. Thank you. Nancy On Wed, Jul 29, 2009 at 7:49 PM, Justin A. Lemkul wrote: > > > Nancy wrote: > >> Hello, >> >> I am trying to run energy minimisation on a

[gmx-users] How to Run Energy Minimisation

Thank you. Nancy ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/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 lis

Re: [gmx-users] MD Simulation of DPPC Lipid Bilayer

ound in residue 17 while adding improper --- Please let me know how I should go about this. Thanks, Nancy On Tue, Jul 28, 2009 at 1:12 PM, Justin A. Lemkul wrote: > Quoting Nancy : > > > Hello, > > > > I am new to Gromacs, but have prior experience with MD simu

[gmx-users] MD Simulation of DPPC Lipid Bilayer

Thank you. Nancy ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/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. Us

Re: [gmx-users] box size changed

ot;. Very grateful for your advice and help!!! Nancy - Original Message - From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Wednesday, February 28, 2007 5:15 PM Subject: Re: [gmx-users] box size changed Nancy Deng w

Re: [gmx-users] box size changed

ion stage, the water particles seems prefer to roam away from the originally centered small molecule, which i guess the reason to increase the overall size of the box... Not sure whether this provides some useful input to help me out of the trouble :) thanks Nancy - Original Mess

[gmx-users] box size changed

fix this??? Whether Gromacs is the right tool to sample small molecule conformational space. I desperatedly need your advice and appreciate your any input!!! Thanks, nancy ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailma