[gmx-users] PubChem Online Compound Search and Download

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 interface or send

[gmx-users] In Silico Compound Library Search

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 or send

[gmx-users] Chelation of Calcium with Citrate

are 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 requests to the 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

[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 listgmx

[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

PM, David van der Spoel sp...@xray.bmc.uu.sewrote: 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 in the region of 800-1400nm

[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-users mailing

[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

Re: [gmx-users] Ice Crystal Structure

Thank you very much for the information. Nancy On 11/29/11, Dallas Warren dallas.war...@monash.edu wrote: http://www.google.com.au/search?q=ice+crystal+coordinate+fileie=utf-8oe=utf-8aq=trls=org.mozilla:en-US:officialclient=firefox-a Second listed item contains (or leads you to where you

[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.gromacs.org

[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] 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] Automated RMSD Calculations

Thanks alot for the info. Nancy On Fri, Mar 25, 2011 at 6:22 PM, Justin A. Lemkul jalem...@vt.edu 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 simple software program or method

[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 archive at http

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 jalem...@vt.edu wrote: Nancy wrote: Hi All, I've used used Gromacs under Linux, and I'm wondering whether it can be used

[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 attachment

[gmx-users] TZD Tautomers

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 attachment: Pioglitazone_Tautomers.png-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Tautomer Prediction

. 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 attachment: Figure_1.gifattachment: Figure_2.gifattachment: Figure_3.gif-- gmx-users mailing listgmx-users@gromacs.org

[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 attachment: Pioglitazone_Tautomers.png-- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Thiazolidinedione Tautomers

, 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 attachment: TZD_Tautomers.png-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Adding Partial Charges for Small Molecules

(and attached as NAD.mol2 with corresponding PNG structure image). Thanks in advance, Nancy @TRIPOSMOLECULE NAD.mol2 70741 0 0 SMALL USER_CHARGES @TRIPOSATOM 1 C1 -1.41175.8700

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 jalem...@vt.edu wrote: Nancy wrote: Hi All, I am trying to add partial charges to nicotinamide adenine dinucleotide (NAD+), for input to molecular simulations. I have been using the UCSF

[gmx-users] Converting SDF to Mol2 Format

to 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

in 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't

[gmx-users] Analyzing Protein-Ligand Interactions

) as 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

[gmx-users] Fatal Error: Segmentation Fault

. 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-requ

[gmx-users] Segmentation Fault Problem

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/listinfo/gmx-users Please search the archive

[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 bruced...@yahoo.com wrote: On Wednesday, August 12, 2009 at 8:47:33 PM, Nancy nancy5vi...@gmail.com wrote: In an earlier message, it was stated that topolbuild

Re: [gmx-users] Fatal Equilibration Errors

force field used? Thank you. Nancy On Mon, Aug 10, 2009 at 6:22 PM, Bruce D. Ray bruced...@yahoo.com wrote: On Sunday, August 9, 2009 at 4:32:19 PM, Nancy nancy5vi...@gmail.com wrote: I obtained the ethylene glycol (1,2-ethanediol) structure from the URL: http://www.rcsb.org/pdb

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 guidance for you in terms

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. pn...@utnet.utoledo.eduwrote: Dear Nancy, It was useful to find charges for the solute... I am not a GROMACS user, so I do not know what

[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 archive

Re: [gmx-users] Force Field Charge Parameters

–10740 Are you suggesting that the authors used incorrect parameters? On Mon, Aug 10, 2009 at 6:05 PM, Justin A. Lemkul jalem...@vt.edu wrote: Nancy wrote: Hello, I have successfully minimised and equilibrated two systems, one consisting of a single molecule of ethylene glycol (1,2

Re: [gmx-users] Fatal Equilibration Errors

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 (based on GROMOS96 53a6) and SPC/E water model? Thank you. Nancy ===ethanediol.top

[gmx-users] Fatal Equilibration Errors

and current coordinates There were 12 inconsistent shifts. Check your topology Segmentation fault === I don't know what is happening wrong. Please advise. Thank you. Nancy ___ gmx-users mailing

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 jalem...@vt.edu wrote: Nancy wrote: Hello, I have successfully minimised and equilibrated ethylene glycol in a water box. I have noticed that there seem

Re: [gmx-users] Fatal Equilibration Errors

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 coulombtype = PME

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

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 bruced...@yahoo.com wrote: On Wednesday, August 5, 2009 at 6:03:51 PM, Nancy nancy5vi...@gmail.com wrote: I am trying to run

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

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 bruced...@yahoo.com wrote: On Thursday, August 6, 2009 at 11:58:20 AM, Nancy nancy5vi

[gmx-users] Very High Forces During Minimisation

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 minimisation. Thank you. Nancy

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

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. Lemkul jalem...@vt.edu

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

the problem might be? Thanks, Nancy On Thu, Aug 6, 2009 at 6:48 PM, Bruce D. Ray bruced...@yahoo.com wrote: On Thursday, August 6, 2009 at 4:08:18 PM, Nancy nancy5vi...@gmail.com wrote: I have attempted to perform energy minimisation from scratch again, and these are the commands that I am

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

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 bruced...@yahoo.com wrote: On Tuesday, August 4, 2009, at 6:30:57 PM, Nancy nancy5vi...@gmail.com wrote: I am trying to simulate a simple system

[gmx-users] Energy Minimisation Values

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/search before posting! Please don't post (un)subscribe

Re: [gmx-users] Energy Minimisation Values

= 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 jalem...@vt.edu wrote: Nancy wrote: Hello, I was trying to run

[gmx-users] Energy Minimisation and Equilibration Problems

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 unstable. Thank you. Nancy

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

=== 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 mailing listgmx-users

Re: [gmx-users] Carbohydrate MD Simulation

you. Nancy On Sat, Aug 1, 2009 at 11:31 AM, Bruce D. Ray bruced...@yahoo.com wrote: On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy nancy5vi...@gmail.com wrote: If it necessary to manually create force field parameters for each molecule, then how can one run a simulation involving a number

[gmx-users] topolbuild1_2_1.tgz decompressing problem

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. Use the www

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 jalem...@vt.edu wrote: Nancy wrote: Hello, I downloaded topolbuild1_2_1.tgz from the URL

[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't

Re: [gmx-users] Carbohydrate MD Simulation

that is 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 jalem...@vt.edu wrote: Nancy wrote: Hello, I am trying to run a MD simulation on trehalose (glucose

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 jalem...@vt.edu wrote: Nancy wrote

[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. Thanks, Nancy

Re: [gmx-users] Viewing Trajectories with VMD

Thanks, it works. Nancy On Thu, Jul 30, 2009 at 7:12 PM, Joshua Adelman jadel...@berkeley.eduwrote: 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 data only

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

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 jalem...@vt.edu wrote: Nancy wrote: Hello, I am trying to run energy minimisation on a lipid bilayer (downloaded from: http

[gmx-users] MD Simulation of DPPC Lipid Bilayer

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. Use the www

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

let me know how I should go about this. Thanks, Nancy On Tue, Jul 28, 2009 at 1:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Nancy nancy5vi...@gmail.com: Hello, I am new to Gromacs, but have prior experience with MD simulations. I'd like to setup and run a simulation

[gmx-users] box size changed

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/mailman/listinfo/gmx-users

Re: [gmx-users] box size changed

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 Message - From: Mark Abraham [EMAIL