[gmx-users] Is there an easy way to increase the energy of bonds, angles, etc?

Hi, all, Is there a way to increase the energy of bonds, angles, etc. without doing it manually? I am looking for a parameter in the mdp file to do this. Your help is greatly appreciated. Sincerely, Audie Arthur "Audie" Roberts 7254 Shoreline Dr. #130 San Diego, CA 92122 cell: 206-850-7

[gmx-users] How to force gromacs to fix all bad bonds and angles in a homology model?

Hi, all, I am looking for a way in gromacs or manually to make all the angles, etc. ideal. Perhaps, there is a way to energy minimize a specific subset of residues or a single residue. Your advice would be greatly appreciated. Sincerely, Art Dr. Arthur Roberts, Ph.D. University of

[gmx-users] Is there a way to calculate the hydrodynamic radius using GROMACS?

Hi, all, I was curious, if there is a way to calculate the hydrodynamic radius of a protein using GROMACS? Much appreciated, Art Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences 9500 Gilman Drive #0703 La Jolla, CA 92093

[gmx-users] Force field parameters for the heme in ff53a6

Hi, All, Does anyone know where the force field parameters for the heme in the ff53a6 force field were obtained? Much appreciated, Art Art Roberts 7254 Shoreline Dr. #130 San Diego, CA 92122 cell: 206-850-7468 email: aroberts99...@yahoo.com skype=aroberts92122 -- gmx-users mailing list

[gmx-users] Is there a way to protonate small molecules with gromacs without editing ffgmx2.hdb file?

Hi, all, Is there a way to protonate small molecules with gromacs without editing ffgmx2.hdb file? Sincerely, Art Art Roberts 7254 Shoreline Dr. #130 San Diego, CA 92122 cell: 206-850-7468 email: aroberts99...@yahoo.com skype=aroberts92122 -- gmx-users mailing listgmx-users@gromacs.

Re: [gmx-users] How to increase the tolerance for conjugate gradient minimization

dominates the energetics. I would appreciate your input. Art On Jun 4, 2010, at 5:45 PM, Mark Abraham wrote: - Original Message - From: Arthur Roberts Date: Saturday, June 5, 2010 4:57 Subject: [gmx-users] How to increase the tolerance for conjugate gradient minimization To: gmx users

[gmx-users] How to increase the tolerance for conjugate gradient minimization

Hi, all, Is there a way to increase the tolerance for Conjugate Gradient energy minimization? It seems that I can only get a Tolerance (Fmax) = 1e-4 emtol doesn't seem to do the trick. I tried several values. Much appreciated, Art Dr. Arthur Roberts, Ph.D. University of California

[gmx-users] After simulated annealing and then energy minimizing, a docked molecule seems to still be distorted?

t the geometry is correct for the docked molecule? I tried reducing the emtol a lot (i.e. 0.0001), but this didn't improve things much. Your help is much appreciated. Art Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences 9

[gmx-users] Is there a way to energy minimize only part of macromolecular structure?

Hi, all, Is there a way to energy minimize only part of the structure? I have made the ndx file, but I am not sure what parameters to use with mdrun. Your help is much appreciated. Art Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and

[gmx-users] I know about improper dihedrals (i.e. gi_1) , etc. Is there a way to keep phenyl rings absolutely flat.

d. I appreciate your ideas. Much appreciated, Art Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences 9500 Gilman Drive #0703 La Jolla, CA 92093-0703 email: aroberts99...@yahoo.com cell: 206-850-7468 skype=aroberts92122 -- gmx-

[gmx-users] I noticed implicit_solvent in the mdout.mdp. Is it going to be implemented soon?

Hi, all, I noticed that there was an implicit_solvent term in the mdout.mdp. However, it didn't seem operative. I am just curious. Is it going to be implemented soon? Sincerely, Art Art Roberts 3950 Mahaila Ave G18 San Diego, CA 92122 cell: 206-850-7468 email: aroberts99...@yahoo.com sk

[gmx-users] Ensemble averaging between two proteins in the same box.

Hi, all, I am trying to do distance restraints under two different conditions of the protein. I have both of these proteins in the same box. Because the experimentally determined distance restraints are from the same signal, there are distance restraints between similar atoms in both st

[gmx-users] Ensemble Averaging

un.pdb. I would like two coordinate files to represent the last frame of mdrun0.trr and mdrun1.trr. Thank you in advance. Much appreciated, Art Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences 9500 Gilman Drive #0703 La Jolla, CA

[gmx-users] Question about distance restraints, energy minimization and time averaging.

Hi, all, This is probably a very simple question. Does time averaging apply, when distance restraints are used during energy minimization (steepest descent or conjugate gradient)? Your input would be greatly appreciated. Art Roberts Dr. Arthur Roberts, Ph.D. University of California, San

Re: [gmx-users] [Fwd: Loss of bonds in HEME iron after pdb2gmx]

Dear Sarada, You need to paramterize the Cysteinyl ligand manually. There are a variety of references in the literature that provide reasonable energies. Below is a pretty good reference. Best wishes, Art 1. Oda, A., Yamaotsu, N., and Hirono, S. (2005) New AMBER force field parameters o

[gmx-users] Is there a way to add protons to all the residues in a pdb file that was run with the protons missing?

Hi, all, This is probably an obvious question. I did a simulation with an ff53a6 force field, which lacks protons on aliphatic side chains. I have pdb coordinates for each time. Is there a way to add protons to the aliphatic side chains. Your input is appreciated. Sincerely, Art Rober

[gmx-users] Is there a way to add protons to all the residues in a given system?

Hi, all, This is probably an obvious question. I did a simulation with an ff53a6 force field, which lacks protons on aliphatic side chains. I have pdb coordinates for each time. Is there a way to add protons to the aliphatic side chains. Your input is appreciated. Sincerely, Art Rober

[gmx-users] time constants on distance restraints between three molecules

Hi, all, Thank you for you input with previous questions. I have have three molecules: A, B, and C. I have distance restraints between A and B, and B and C. I was wondering, if there is a way to put a different time constant for the distance restraint between A and B than B and C. You

Re: [gmx-users] Constraints - PMF - Different Molecules

Dear Eudes, You need to technically make it 1 "big molecule". As long as there are no bonds specified between molecule A and B. The big molecule will behave as if there are two molecules in it. I do it to dock small molecules to proteins. Steps running Gromacs 3.3.3: 1) Combine molec

Re: [gmx-users] how to write .top file for a rigid molecule

Dear Jinyao, If you are talking about making the ring rigid and side group rigid, I would suggest adding a bunch of improper dihedrals to keep the molecule rigid. I found without adding the improper dihedrals that molecules that I would expect to be rigid were uncharacteristically confor

[gmx-users] appropriate time constant and forces for distance restraints

Hi, all, Question #1: Appropriate time constant for distance restraints. I am docking a small molecule to a macromolecule and I was wondering what would be an appropriate value for a time constant. I was thinking that a time constant that is equal to the time for a single rotation woul

[gmx-users] Is there a way to measure the shortest distance between two groups of atoms?

Hi, all, I was wondering if there is a way to measure the shortest distance between two groups of atoms? g_dist seems to only measure the average distance between the two groups. Your input would be greatly appreciated. Sincerely, Art Roberts

[gmx-users] Does gromacs simulate rotation correctly?

Hi, all, Just curious. Does gromacs simulate rotation correctly? From my observation, it would appear that every object in the simulation both small and large has a similar rotational correlation time, which is not reality. I would expect water for example to have an extremely short ro

[gmx-users] Using MPI gromacs with CONDOR

Hi, all, I was wondering if there was anyone out there that has successfully used Gromacs, MPI, and CONDOR. One thing that would be particularly useful would be submit scripts. I have installed MPI on my own account, but I haven't figured out how to use MPI with condor. I would appreci

[gmx-users] Opinion: Can position restraining waters increase the speed of the md simulation?

Hi, all, In a previous email, I asked about the availability of implicit water calculations in Gromacs 4.0, which might be available in Gromacs 4.1. In the meantime, I was wondering if I position restrained waters that are 6 Angstroms from the protein, would that increase the speed of md

[gmx-users] Is the new version of Gromacs going to be able to do implicit water md?

Hi, all, I know this question might seem almost heretical because I am aware of the issues with implicit water md. I actually prefer explicit waters because I think it more realistically represents the water environment. However, the problem with explicit waters is that the calculation

Re: [gmx-users] rtp

Dear Jayant, I might be wrong, but I think the original gmx force field that you are referring to has been deprecated. Best wishes, Art On Dec 14, 2007, at 1:44 PM, jayant_jacques wrote: Hi! I am attempting to simulate a protein with a modified amino acid using the Gromacs force field wi

[gmx-users] Is there any way to do r^3 distance dependence?

Hi, all, I know that Gromacs has the capability of restraining a molecule with r^6 distance dependence. Is there any way to do r^3 distance dependence? Best wishes, Art Roberts University of Washington Department of Medicinal Chemistry Seattle, WA 98195 ___

Re: [gmx-users] ffamber_chcl3.gro

Check out the gromacs examples in the ../share/gromacs/top for the format. spc.itp water parameters spc216.growater coordinates methanol.itp methanol parameters Best wishes, Art On Dec 4, 2007, at 5:32 PM, Dallas B. Warren wrote: So this means that f

Re: [gmx-users] Change in distances between two atom during MD

Hello, I wrote a python script to do this. I would used pymol. Number each of the pdb files 0ps.pdb 00250ps.pdb, etc. Also, remove the water. Just save the file as distances.py and run in pymol. from pymol import cmd cmd.reinitialize() Distances=[] Line='' TimeMax=11500 TimeIncr=0

[gmx-users] Do you need to have the parameters numbered in order?

To Whom It May Concern: Do you need to have the parameters numbered in order? For example: [ bonds ] ; aiaj functc0c1 c2c3 1 2 2 gb_16 ; CR6 (CR1) CR6 (CR1) 1.41611228368 Angstroms 1 6 2 gb_16 ; CR

[gmx-users] What are lines for g_sas -or file.xvg not g_sas -o file.xvg?

ng like: time hydrophobic-SAS hydrophilic-SAS total-SAS hydration-free-enthalpy Cheers, Tsjerk On 5/4/07, Arthur Roberts <[EMAIL PROTECTED]> wrote: This is a question about what the lines from the solvent accessibility mean. I executed the following command. g_sas -s mdrun.tpr -f m

[gmx-users] g_sas

This is a question about what the lines from the solvent accessibility mean. I executed the following command. g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg xmgrace -nxy mdrun.xvg I get two sets of values: one is bigger (black) than the other (red). Is the red lower value, the standard erro

[gmx-users] How can I make commands non-interactive?

Hi, all, I need to be able to execute commands by a script and I need the commands to be non-interactive. One example of the commands that I use is g_rms. How can I make this command totally non-interactive? Thank you in advance, Best wishes, Art Roberts University of Washington Department of

[gmx-users] I need to string together a bunch of g_rms's

Hi, all, I need to know the rms deviation of the backbone from the beginning of my simulation to the end. I had to split the simulation into 250ps segments. Total simulation time is 10 ns. Is there a way to determine the g_rms of the whole simulation (10 ns) or to string the values together fro

[gmx-users] Trouble getting Gromacs 3.3.1 to see libgm.so.0

Hi, all, I am attempting to compile Gromacs 3.3.1 on a 256 node IBM Netfinity 4500R with Redhat 8.0. Despite pointing to the library as suggested by Carsten Kutzner. i.e. setenv CPPFLAGS '-I/users/aroberts/fftw3/include -I/usr/local/gm-1.6.5/include' setenv LDFLAGS '-L/users/aroberts/fftw3/lib -

[gmx-users] Problems Installing on IBM Netfinity 4500R with Redhat 8.0

Hi, all, I am attempting to compile Gromacs 3.3.1 on a 256 node IBM Netfinity 4500R with Redhat 8.0. I already checked the mailing lists and the web a couple of times. Below is my configuration file, the output, and the config.log. I would appreciate any input into this greatly. Best wishes, Ar

Re: [gmx-users] Is there any way to put dummy atoms into the n2t file of the CVS version of Gromacs?

words, H2, which I specified as an alkene proton, still works as a proton in most molecular modeling packages. Best wishes, Art --- David van der Spoel <[EMAIL PROTECTED]> wrote: > Arthur Roberts wrote: > > Hi, all, > > > > I am interested in putting specific atom

[gmx-users] Is there any way to put dummy atoms into the n2t file of the CVS version of Gromacs?

Hi, all, I am interested in putting specific atom types into my n2t file in the CVS version of gromcas for use in x2top. For example, in Gromacs 3.3.1, I used H2 to denote alkene proton and H3 to denote an alkyne proton. However, in the CVS version of gromacs, I am not able to do that. I

Re: [gmx-users] x2top doesn't seem to recognize connectivity in the n2t file

Thanks, David. I will try it out and tell you how the results went. Best wishes, Art --- David van der Spoel <[EMAIL PROTECTED]> wrote: > Arthur Roberts wrote: > > Hi, all, > > > > I have been trying to convert a small molecule > into > > oplsaa format

[gmx-users] x2top doesn't seem to recognize connectivity in the n2t file

Hi, all, I have been trying to convert a small molecule into oplsaa format using the x2top. The x2top doesn't seem to recognize the connectivity specified in the n2t file. Below is the n2t file ; alkanes (first number is bond type and second number is number of protons) C opls_138

[gmx-users] gromacs 3.3.1 with fftw 3.12 and the current version of AIX 5.2

Hi, all, Has anyone out there successfully compiled gromacs 3.3.1 with fftw 3.12 and the current version of AIX 5.2 on a Bluegene server? I am not sure how the environment variables should be set. Your input would be much appreciated. Best wishes, Art __

[gmx-users] Making small molecule topology files

Hi, all, I would like to make a small molecule using the OPLSAA force field. Is there a simple way to do it (i.e. a program that makes the topology file) or do I have to manually type the OPLSAA topology file? Thank you in advance, Art ___ gmx-use

[gmx-users] Question about scaling charges

Hi, all, I was talking to a friend of mine that works in an MD lab. He said that the charges from QM/MM or semiempirical need to be scaled to charges in the force field. For example, a heme will have specific charges in the force field, while hemes that represent different bound states may

Re: [gmx-users] Configuration on an IBM power computer

Hi, Volker I have installed Gromacs 3.3.1 on a couple of IBM power computers (i.e. P655+). You need to install fftw3, and not fftw 2.15. fftw 2.15 didn't seem to work with AIX 5.2. Here are the instructions: Installing fftw3 setenv MPICC 'mpcc_r -q64' setenv CC 'xlc_r -q64' setenv F77 'xlf_

Re: [gmx-users] simulation at particular pH

Hi, Luisa, I would first calculate the number of protons (H+) that you would find your water box. Then I would use the command genion to generate that number of H+'s that corresponds to the pH. Then I would use grompp to find out what the final charge is. If it is still negative, I would add NA+

Re: [gmx-users] help with distance restraints

Hi, Michael, 1) add Cu2+ the [atoms], [bonds], etc sections in the .top file. 2) you need to change all the entries in the residue column of the [atoms] section to the same name (e.g. MOL) in both the top file and the gro file, including all the residues of the protein. Gromacs needs to think tha

Re: [gmx-users] mdrun hangs on nodes of P655+ aix 5.2

I had the same problem as Arthur Roberts. So I > downloaded your new > version of gmx_system_xdr.h and gmx_system_xdr.c > from > http://bugzilla.gromacs.org/show_bug.cgi?id=55 > > Before I recompile gromacs, I checked the difference > between your new > version and the old o

[gmx-users] Pressure coupling appears to produce errors on the P655+ aix 5.2

Hi, All, I would like to thank Carsten Kutzner, Erik Lindahl, and David van der Spoel for their advise with my previous problem with not getting any data with mdrun. It turned out to be due to the fourier spacing and the PME order. In addition, David van der Spoel's suggestion of using a water s

[gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Hi, all, I am trying to run Gromacs on a P655+ with Aix 5.2. Initially, mdrun appears to work, but always hangs. Eventually, I get timed out from the supercomputer with no data to show for it. Below is a link detailing the problem: http://cetus.mchem.washington.edu/pub/supercomputer/Mdrun-hang

[gmx-users] mdrun hangs on nodes of P655+ aix 5.2

Hi, all, I am trying to run Gromacs on a P655+ with Aix 5.2. Initially, mdrun appears to work, but always hangs. Eventually, I get timed out from the supercomputer with no data to show for it. Below is a link detailing the problem: http://cetus.mchem.washington.edu/pub/supercomputer/Mdrun-hang

Re: [gmx-users] Problems Installing Gromacs 3.3.1 on AIX 5.2

wishes, Art --- David van der Spoel <[EMAIL PROTECTED]> wrote: > Arthur Roberts wrote: > > To Whom It May Concern: > > > > I have checked the archives, but I have not found > a > > good solution for the following problem: > > > > When I try to compil

[gmx-users] Problems Installing Gromacs 3.3.1 on AIX 5.2

To Whom It May Concern: I have checked the archives, but I have not found a good solution for the following problem: When I try to compile Gromacs 3.3.1, I get complaints from the compiler that I have undefined symbols. The symbols are present in the libraries, so I don't know why ld can not see