[gmx-users] membrane protein simulation
Title: membrane protein simulation Hi gmx-users I am trying to set up an ED experiment with the low resolution structure of a membrane protein in the hope of generating NMR-like structures. >From what I have read until now, I know that I should either restrain the transmembrane domain of the enzyme (or simulate without it), or do the simulation within a bilayer membrane. The choice is somewhat complicated by the fact that the active site of the protein (which is of interest to me) is quite close to the transmembrane domain. So I think it would be safer to simulate with the membrane, or is there a simpler solution ? Also, I am quite new to membrane protein simulation and I would like to know how the bilayer type is chosen ? (My protein is a eukaryotic enzyme naturally bound to the endoplasmic reticulum). Any help will be apreciated. Diane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] binding free energy calculations on charged ligands
Hello all, I'm still trying to get the binding free energy for my ligands, and I now think I will have to do another simulation, since my first one used PME and I didn't record velocities in my trajectory. But first I need some advice, since I can't find a paper which describes unambiguously what I want to do. First, my ligand is charged (carboxylate) ; what is the best (and easiest) method to calculate the binding free energy for charged ligands ? Is MM-PBSA preferable to LIE in that case ? I tried LIE with PME, and I know that you can get the PME contribution by doing a mdrun -rerun with zero charge on all charge groups alternatively. I also understand that this was described in the mail archive, but I can't find the mails in question. Can somebody tell me exactly when those mails were written ? And do the 'standard' settings for PME (as described in the manual) need to be changed ? I understand that the Coul-LR and LJ-LR terms are not produced when rcoulomb = rlist and rvdw = rlist respectively ? Or those are the terms that are calculated in the zero-charged reruns ? Also, what is to be done with the counterions ? Since it does not seem possible to have an equilibrium distribution in a reasonable time (on a ns scale), must I run the simulations without them ? All advice will be very appreciated. Diane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE : [gmx-users] *.xvg to jpeg/pdf/png
Hi Arindam To read *.xvg files you need the xmgrace software, which is distributed free of charge, sometimes as a rpm depending on your linux version. It is also available for Cygwin, but I have never managed to make it work. Once you have opened the *.xvg file in xmgrace (xmgrace *.xvg), you need to open the print setup menu, select the wanted print format (you can have .jpg, .ps and a few others) and specify the path and file name. Then you select "print". The file should have appeared in the selected directory. Hope this helps Diane De: [EMAIL PROTECTED] de la part de Arindam Ganguly Date: jeu. 2006-08-17 13:06 À: gmx-users@gromacs.org Objet : [gmx-users] *.xvg to jpeg/pdf/png Hi gmx-users, i have a energy.xvg file, but i am not able to convert it to a jpeg, pdf or png format. in fact any cross platform format so that i can print out or send it for publications. any help in this regard is welcomed. thanks. arindam <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Ligand binding energy using LIE with PME
On the same subject, I have read in the list about long-range interactions (Coul-LR, LJ-LR) which are supposed to be included in the energy parameters calculated in g_energy, but I never see those. Do you have to write something specific in the .mdp files to get them ? Also, some of my inhibitors and complexes are charged. In my simulation of the complex, I have added a counterion (Na). Does this complicate matters worse ? For the inhibitors in water, I protonated the ligand, according to a procedure I saw in a paper. Would it be simpler, in the case of the complexes, to protonate one residue away from the active site ? -Original Message- From: [EMAIL PROTECTED] on behalf of Diane Fournier Sent: Wed 8/16/2006 10:10 AM To: gmx-users@gromacs.org Subject: [gmx-users] Ligand binding energy using LIE with PME Hi gmx-users I know that this has been discussed before from consultation of the mail archive, but there is still confusion : I want to obtain the ligand binding energy from my 1ns PME simulation of a ligand-protein complex. I have made, as directed, a simulation (with PME) of the ligand in water to calculate Eqq and Elj. I am not using the g_lie program since I know I will need to mind the PME contribution. I'm using (I hope I am correct) the average values of all ligand-protein (Coul-SR, Coul-14, LJ-SR, LJ-14) and ligand-rest (Coul-SR, Coul-14, LJ-SR, LJ-14) terms for the ligand complex simulation and all ligand-solvant terms (same) from the ligand in water simulation. In my case the 1-4 and ligand-rest terms are equal to zero, which I think is normal as no 1-4 interactions are defined between ligand and protein (since they are not covalently bonded) and that no restraints are applied. It is for the so-called PME long-range contribution that I get confused. I have done a mdrun -rerun of my trajectory using a .tpr file where the ligand has zeroed partial charges for both simulations. From what I understood, the same energy terms as mentionned above have to be extracted from these rerun simulations and substracted from the previous terms as they represent what the ligand "feels" from PME from the image systems around the box. In my case, these contributions are very small (< 1kJ/mol), which I think is due to the fact that I am using a box size (d = 0.85nm for the protein, d = 2.0nm for the ligand) which is supposed to make PME artifacts negligible. I am just wondering if this is correct so far, or if I need to do other rerun simulations with zero charge on protein and solvant to obtain the PME contribution. Any input will be appreciated Diane <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] steroid topology
I am also working with steroids (but in my case, steroidal hybrid inhibitors) with the gmx force field. From my experience working with the PRODRG program, the topologies needed some modifications (for example the program assigns my phenol OH as a carbonyl and one aromatic bare carbon as a CH1) and produce strange partial charges for the steroid which are not reproduced for different inhibitors with the same steroid moiety. Maybe you should try assigning partial charges using a reliable method (ex with bcc in antechamber) to see if that is the problem (but I think that is unlikely). If you are seeing that same behavior in a steepest descent minimization step, there can be an error in the bonding scheme (check the bonding section of your topology) or a missing improper dihedral parameter. Diane -Original Message- From: [EMAIL PROTECTED] on behalf of dhruva chakravorty Sent: Tue 8/15/2006 6:13 PM To: gmx-users@gromacs.org Subject: [gmx-users] steroid topology Hello, I have been having trouble with a topology I created for androst-5-ene-3,17-dione (GROMOS 96 force field). I have found the molecule to bend inwards withing 100 ps of equilibration, something which has not been seen by others who have used CHARMM or AMBER. I have also tried to convert the topology generated by the PRODRG DUNDEE server for GROMACS but had the same issues with it. Can anyone throw any pointers my way, or better still a steroid topology which works Regards Dhruv __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Ligand binding energy using LIE with PME
Title: Ligand binding energy using LIE with PME Hi gmx-users I know that this has been discussed before from consultation of the mail archive, but there is still confusion : I want to obtain the ligand binding energy from my 1ns PME simulation of a ligand-protein complex. I have made, as directed, a simulation (with PME) of the ligand in water to calculate Eqq and Elj. I am not using the g_lie program since I know I will need to mind the PME contribution. I'm using (I hope I am correct) the average values of all ligand-protein (Coul-SR, Coul-14, LJ-SR, LJ-14) and ligand-rest (Coul-SR, Coul-14, LJ-SR, LJ-14) terms for the ligand complex simulation and all ligand-solvant terms (same) from the ligand in water simulation. In my case the 1-4 and ligand-rest terms are equal to zero, which I think is normal as no 1-4 interactions are defined between ligand and protein (since they are not covalently bonded) and that no restraints are applied. It is for the so-called PME long-range contribution that I get confused. I have done a mdrun -rerun of my trajectory using a .tpr file where the ligand has zeroed partial charges for both simulations. From what I understood, the same energy terms as mentionned above have to be extracted from these rerun simulations and substracted from the previous terms as they represent what the ligand "feels" from PME from the image systems around the box. In my case, these contributions are very small (< 1kJ/mol), which I think is due to the fact that I am using a box size (d = 0.85nm for the protein, d = 2.0nm for the ligand) which is supposed to make PME artifacts negligible. I am just wondering if this is correct so far, or if I need to do other rerun simulations with zero charge on protein and solvant to obtain the PME contribution. Any input will be appreciated Diane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] problem with ambconv
Thanks, yes, that would be interesting as I plan on obtaining AMBER. Does it work with any version ? Diane -Original Message- From: [EMAIL PROTECTED] on behalf of David Mobley Sent: Fri 8/4/2006 3:00 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] problem with ambconv Diane, We have an in-house script called amb2gmx written in collaboration with the Pande group that works for this purpose, although it requires an installation of AMBER. Let me know if you would like it. Thanks, David On 8/4/06, Diane Fournier <[EMAIL PROTECTED]> wrote: > > > > Hi > > I'm presently trying to use the ambconv program to convert amber topologies > generated with antechamber v. 1.26 and tleap to gromacs format for use with > the amber force field port. > > The problem is, I can't get the program to work. For example : > > $ ambconv -v -at spl2.atop -rst spl2.rst -gt spl2.itp -gro spl2.gro -pdb > spl2.pdb > AMBCONV v1.0 > AMBER .top : spl2.atop > AMBER .rst : spl2.rst > GROMACS .top : spl2.itp > GROMACS .gro : spl2.gro > PDB .pdb : spl2.pdb > Segmentation fault > > This is using the old file format generated with tleap when setting > oldprmtopformat to on. The same happens with the new file formats (.prmtop > and .inpcrd). > I have tried modifying the ambconv.c file and recompiling as suggested in > the mailing list (Wed Jun 16 18:41:55 CEST 2004), but got the same result. > > Does someone has a version of ambconv which works with antechamber 1.26, or > should I use an older version of antechamber and leap ? > > Diane > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with ambconv
Title: problem with ambconv Hi I'm presently trying to use the ambconv program to convert amber topologies generated with antechamber v. 1.26 and tleap to gromacs format for use with the amber force field port. The problem is, I can't get the program to work. For example : $ ambconv -v -at spl2.atop -rst spl2.rst -gt spl2.itp -gro spl2.gro -pdb spl2.pdb AMBCONV v1.0 AMBER .top : spl2.atop AMBER .rst : spl2.rst GROMACS .top : spl2.itp GROMACS .gro : spl2.gro PDB .pdb : spl2.pdb Segmentation fault This is using the old file format generated with tleap when setting oldprmtopformat to on. The same happens with the new file formats (.prmtop and .inpcrd). I have tried modifying the ambconv.c file and recompiling as suggested in the mailing list (Wed Jun 16 18:41:55 CEST 2004), but got the same result. Does someone has a version of ambconv which works with antechamber 1.26, or should I use an older version of antechamber and leap ? Diane ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] does gromos force field can explain pi-pi interaction
Yes,
this looks like the force field application of the Hunter point-charge model
(J. Am. Chem. Soc.; 1990; 112(14); 5525-5534). This force field could
theoretically be used to model pi-stacking in proteins, as a more
computationally economical procedure compared to QMMM. Unfortunately, I dont
think it has been ported to Gromacs yet ...
Diane
-Original Message-
From: [EMAIL PROTECTED] on behalf of andrea spitaleri
Sent: Thu 7/27/2006 6:26 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] does gromos force field can explain pi-pi interaction
> None of the MM force field can reproduce pi-pi interactions
> for the simple reason that the force field does not
> describe electrons explicitly !! That is the case for
> most of the interactions involving electrons !!
What about XED forcefield??
An Evaluation of Force-Field Treatments of Aromatic Interactions
Chemistry - A European Journal
Volume 8, Issue 13 , Pages 2860 - 2867
Gianni Chessari, Dr. 1, Christopher A. Hunter, Prof. 1 *, Caroline M. R. Low,
Dr. 2, Martin J.
Packer, Dr. 1, Jeremy G. Vinter, Dr. 2, Cristiano Zonta
Regards
andrea
--
---
Andrea Spitaleri
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
---
Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria")
il codice fiscale della
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a [EMAIL PROTECTED] o vai sul sito
www.5xmille.org
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
<>___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] does gromos force field can explain pi-pi interaction
I have read a lot on this subject since I wanted to prove one such interaction myself (between inhibitor and enzyme). Generally, authors who talk of such interaction never give proof using simulation, but use a simple geometric criteria (benzene rings are superposed in T-shape or face-to-face staggered configuration at a given distance) to describe them in crystal structures. For modeling, there are a few papers (beginning 1990s, not quite recent) which used a point charge model to model pi-pi stacking (Hunter-Saunders model). In this model, charges are distributed onto the hydrogens and in the middle of the benzene ring (with a dummy atom) and their results (geometry optimization) showed some similarity to experimental results seen in crystals. I can give you the references if you like. However, pi-pi interactions have some polarization component, and so they have been best modeled with quantum mechanics; this would involve doing a QMMM simulation. I have not seen yet a paper talking about QMMM simulation of pi-pi stacking (if somebody has seen one please give me the reference) I have also heard of polarizable force fields, but I don't know if they can model pi-stacking properly. If somebody has heard of a proven method of modeling pi-stacking, energy- and geometry-wise, I would also be very interested in it. Diane -Original Message- From: [EMAIL PROTECTED] on behalf of Wei Fu Sent: Wed 7/26/2006 11:44 AM To: gmx-users@gromacs.org Subject: [gmx-users] does gromos force field can explain pi-pi interaction Dear gmx users, My simulation shows that the aromatic ring of ligand forms stacking pi-pi interaction with the side chain of Phe of receptor during MD simulation. One reviewer of my manuscript questions that such pi-pi interaction can not accurately accounted for by the employed force field. I do not know how to answer this question, any idea is highly appreciated! Linda ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] MPI gromacs usage
Hi gromacs users I've already used gromacs single-processor version and I want to use the parallel version of gromacs on a SGI Altix 2700 with 32 processors. I'm wondering how to proceed, because this does not seem to be explained properly anywhere. Do I have to give special instructions in grompp to split the simulation on several processors, or can I use the same .tpr file I'm using with the single-processor version of mdrun ? Thank you___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] prodrg and charge groups
Title: prodrg and charge groups I don't know if this has already been discussed, but I'm wondering how the charges and charge groups are assigned by PRODRG. I'm curious about this because I have been using it for a few similar ligands which all contain a steroid (estradiol) moiety. In the three cases, the charge groups and charges that were assigned were quite different for the estradiol part. Also, when compared to the partial charges found for the phenol group of tyrosine in the amino acid topologies, the phenol group charges for estradiol make no sense (they should be quite similar, right ?). What I've been doing until now is to modify the charges and charge groups so that they are identical for the estradiol moiety in all cases (so that this part displays the same behavior in all simulations). Is this the right way to proceed ? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE : [gmx-users] Does Gromacs work on a molecule w hich is not protein
For molecules which are not amino acids, DNA or RNA, you have to write a topology yourself. There are some tools that can help you with that. If you plan to use the gromacs united-atom forcefield (ffgmx), you can try PRODRG, which is available on the Dundee server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/). It will give you a .itp file (information on the molecule itself) to which you will have to add some system information (some includes, like forcefiled type, water .itp file, etc). The format of the .top file is given in the user's manual. But be careful to edit the file PRODRG gives you, because sometimes there are errors in the atom types assignation and in the partial charges that are given (you can compare with charges calculated with a quantum mechanical software, like Gaussian or MOPAC). If you plan to use another forcefield, you will have to write the topology yourself (atom types & charges, bond parameters, angle parameters, dihedrals and improper), using the descriptions of the atom types given in the forcefield's .atp file. Check also in the contributed software section for some programs that can convert one format of topology (ex.: AMBER or TINKER) to gromacs format. The .pdb file can be transformed into a .gro using the editconf program. Hope that helps Diane De: [EMAIL PROTECTED] de la part de Tanping Li Date: mer. 2006-05-17 10:58 À: Discussion list for GROMACS users Objet : [gmx-users] Does Gromacs work on a molecule which is not protein Dear all, I plan to run solvate a small molecule using Gromacs. This small molecule is not a protein or DNA or RNA. So I meet the problem at the first step to run pdb2gmx, the wrong information says Gromacs can't recognize this molecule. Is there a way to assign charge to this small molecule and get a *.top file; could I use gromacs to run this unknown small molecule? Thank you very much for your suggestion. I have bothered by this for a while. Best Tanping ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE : [gmx-users] Fatal error: moleculetype S OL is redefined.
I had the same problem once, and it turned out that I had mistakenly put information about my ligand molecule in the "moleculetype" section of my enzyme topology file. That info is also given in the .itp files that are included into your peptide topology file (at the end of the file for ions and solvent), so grompp sees two definitions for the same molecule type. The number and type of solvent molecules must be included in the "molecule" section of the topology (completely at the end of the the .top file). What is strange, though, is that genbox usually puts that information automatically in the .top file that it generates. My advice is to check your topology file. Diane De: [EMAIL PROTECTED] de la part de Absalom Zamorano Date: mar. 2006-05-09 09:01 À: gmx-users@gromacs.org Objet : [gmx-users] Fatal error: moleculetype SOL is redefined. Hi gromaxers, I want to generate a tpr file for a minimization. I have 3 peptides in water and Im using OPLS ff, but after I run grompp, system backs me the next message: -- creating statusfile for 1 node... checking input for internal consistency... calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours for Protein_X 1 Cleaning up temporary file gromppDDYIem --- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 887 Fatal error: moleculetype SOL is redefined -- Some commentary will be very appreciated. Thank you for advance. Dr. Absalom Zamorano Carrillo Profesor Titular A Programa Institucional de Biomedicina Molecular, ENMyH-IPN Guillermo Massieu Helguera #239 Fracc. "La Escalera" Ticomán, D.F. México, C.P 07320 Tel. (55) 57296000, ext 55542 ___ Do You Yahoo!? La mejor conexión a Internet y 2GB extra a tu correo por $100 al mes. http://net.yahoo.com.mx ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] ligand falling out of active site during EM
Thank you ! I think the problem was indeed with building the box, because I redid the whole sequence on my drug-enzyme system (building the box with editconf, putting the water with genbox, and then writing my .tpr file with grompp) and ran the same (test) position restraint md run, and this time, the ligand was inside. Will try minimisation again. Diane -Original Message- From: [EMAIL PROTECTED] on behalf of David Mobley Sent: Mon 5/8/2006 12:22 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] ligand falling out of active site during EM Diane, On 5/8/06, Diane Fournier <[EMAIL PROTECTED]> wrote: > Still on the same problem, I made a pr run on the complex, and had the same > result (ligand is out of the active site at time = 0.000 ps. Then I ran the > same pr run, but with dt = 0.001 ps with all coordinates output for my > trajectory. It turns out the ligand starts out of the active site, even if my > input coordinates have the ligand inside. What is happening ?? First, if you are doing energy minimization, dt does nothing... But second, double-check where it starts. For example, generate a tpr file and then use trjconv to convert your initial gro file to a pdb file and open it up with some viewer (i.e. pymol) (Or I guess use vmd to visualize your starting gro file). See if the ligand starts outside the binding site. If so, then it probably means you've done something in a funny order. For example, if you use editconf and genbox on just the protein before adding the ligand, well, those tools re-center teh protein in the box, so it will get shifted relative to the ligand (and hence the ligand will no longer be in the binding site). I think the solution to that is to use editconf or genbox on the system (protein+ligand), not just the protein. If that isn't the problem, it might be worth e-mailing the list exactly the steps you're following, and double-checking that the initial protein and ligand coordinates prior to setting up the system in GROMACS have the ligand in the binding site. David > > > -Original Message- > From: [EMAIL PROTECTED] on behalf of Diane Fournier > Sent: Fri 5/5/2006 3:05 PM > To: gmx-users@gromacs.org > Subject: [gmx-users] ligand falling out of active site during EM > > Hello ! > > I'm trying to run a molecular dynamics on a drug-enzyme complex. I did John > Kerrigan's tutorial and everything worked fine. Now I'm trying with my system > but I get a problem : the ligand keeps falling out of the active site during > EM. I thought maybe it was a pbc problem and used comm-grps = protein in my > .mdp file, but I get the same result. I transformed the .gro input file to > .pdb to view it in pymol and the ligand is in the active site before > simulation. So it seems this happens during steepest descents EM. > > The ligand is a hybrid inhibitor containing a steroid moiety (estradiol) > linked to an adenosine-like moiety with a 13-methylene alkyl chain. > > Is there a way to keep/force the ligand in the active site during EM (maybe > using PR) ? > > Is this reflecting some physical phenomenon, ie the ligand has low affinity ? > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] ligand falling out of active site during EM
Still on the same problem, I made a pr run on the complex, and had the same result (ligand is out of the active site at time = 0.000 ps. Then I ran the same pr run, but with dt = 0.001 ps with all coordinates output for my trajectory. It turns out the ligand starts out of the active site, even if my input coordinates have the ligand inside. What is happening ?? -Original Message- From: [EMAIL PROTECTED] on behalf of Diane Fournier Sent: Fri 5/5/2006 3:05 PM To: gmx-users@gromacs.org Subject: [gmx-users] ligand falling out of active site during EM Hello ! I'm trying to run a molecular dynamics on a drug-enzyme complex. I did John Kerrigan's tutorial and everything worked fine. Now I'm trying with my system but I get a problem : the ligand keeps falling out of the active site during EM. I thought maybe it was a pbc problem and used comm-grps = protein in my .mdp file, but I get the same result. I transformed the .gro input file to .pdb to view it in pymol and the ligand is in the active site before simulation. So it seems this happens during steepest descents EM. The ligand is a hybrid inhibitor containing a steroid moiety (estradiol) linked to an adenosine-like moiety with a 13-methylene alkyl chain. Is there a way to keep/force the ligand in the active site during EM (maybe using PR) ? Is this reflecting some physical phenomenon, ie the ligand has low affinity ? <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ligand falling out of active site during EM
Title: ligand falling out of active site during EM Hello ! I'm trying to run a molecular dynamics on a drug-enzyme complex. I did John Kerrigan's tutorial and everything worked fine. Now I'm trying with my system but I get a problem : the ligand keeps falling out of the active site during EM. I thought maybe it was a pbc problem and used comm-grps = protein in my .mdp file, but I get the same result. I transformed the .gro input file to .pdb to view it in pymol and the ligand is in the active site before simulation. So it seems this happens during steepest descents EM. The ligand is a hybrid inhibitor containing a steroid moiety (estradiol) linked to an adenosine-like moiety with a 13-methylene alkyl chain. Is there a way to keep/force the ligand in the active site during EM (maybe using PR) ? Is this reflecting some physical phenomenon, ie the ligand has low affinity ? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE : RE : [gmx-users] segmentation fault in mdrun when using PME
It seems that in my case this is a bug (see Bugzilla, bug # 74) related to using the Intel Math Kernel Library (MKL) v. 8.0.1 for Fourier transforms. The team managing the Altix are trying different FFT libraries. Eric Lindahl says that using a FFT library that is not optimized for Itanium 2 shouldn't hamper the perfomance very much since FT doesn't represent a very big part of the computation. I think the error I get with the version compiled without Fortran is boggus, because this tutorial (John Kerrigan's) was tried sucessfully by many people, so there shouldn't be any mistakes in the .mdp file. Also, the runs I do with that version have strange output and anyway, I don't get that error with the Fortran-enabled version. Segmentation fault has been documented in the position restrained dynamics stage of this tutorial with gromacs 3.3.0 though, and was solved when upgrading to 3.3.1. An exploding system is often caused by extreme forces due to bad contacts, which can be relieved by a minimization step. Have you used a steepest descents minimization step on your system before doing the pr ? De: [EMAIL PROTECTED] de la part de Arneh Babakhani Date: mar. 2006-05-02 23:21 À: Discussion list for GROMACS users Objet : Re: RE : [gmx-users] segmentation fault in mdrun when using PME Hello, I'm experiencing the exact same problem, when trying to do some restrained molecular dynamics of a small peptide in a water box. Have you had any luck in trouble-shooting this? (I've pasted my mdp file below, for your reference). Also running Gromacs 3.3.1 Arneh title = ResMD warnings = 10 cpp = /usr/bin/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 25000 ; total 50.0 ps. nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein sol ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Diane Fournier wrote: De: [EMAIL PROTECTED] de la part de David van der Spoel Date: lun. 2006-05-01 13:33 À: Discussion list for GROMACS users Objet : Re: [gmx-users] segmentation fault in mdrun when using PME Have you enabled fortran at the compilation stage? In that case try it without, otherwise please file a bugzilla, such that we can document this problem (and try to fix it of course). Still doesn't work. logfile ends in the usual way. Except this time, I get this output: Reading file trp_em.tpr, VERSION 3.3.1 (single precision) Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 500 Warning: 1-4 interaction between 1 and 7 at distance 39513.957 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.1# Wrote pdb files with previous and current coordinates and then these files get written: step0.pdb #step0.pdb.1# step-1.pdb step1.pdb Will file a bugzilla. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _
RE : [gmx-users] segmentation fault in mdrun when using PME
De: [EMAIL PROTECTED] de la part de David van der Spoel Date: lun. 2006-05-01 13:33 À: Discussion list for GROMACS users Objet : Re: [gmx-users] segmentation fault in mdrun when using PME Have you enabled fortran at the compilation stage? In that case try it without, otherwise please file a bugzilla, such that we can document this problem (and try to fix it of course). >Still doesn't work. logfile ends in the usual way. Except this time, I get >this output: > Reading file trp_em.tpr, VERSION 3.3.1 (single precision) Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 500 Warning: 1-4 interaction between 1 and 7 at distance 39513.957 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.1# Wrote pdb files with previous and current coordinates and then these files get written: step0.pdb #step0.pdb.1# step-1.pdb step1.pdb Will file a bugzilla. >> >> >> >> >> >>___ >>gmx-users mailing listgmx-users@gromacs.org >>http://www.gromacs.org/mailman/listinfo/gmx-users >>Please don't post (un)subscribe requests to the list. Use the >>www interface or send it to [EMAIL PROTECTED] >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] segmentation fault in mdrun when using PME
-Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: > Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex > molecular dynamics simulation. I have tried doing John > Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation > fault and core dump at the steepest descents minimization step. However, > mdrun works fine when using cutoff instead of PME. > > I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel > Itanium 2 processors (but I'm currently using a single node, so it's not > a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel > Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized > for Itanium 2). > > the em.mdp file looks like: > > title = drg_trp > cpp = /usr/bin/cpp > define = -DFLEX_SPC > constraints = none > integrator = steep > dt = 0.002; ps ! > nsteps = 500 > nstlist = 10 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb= 0.9 > rvdw= 0.9 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft= yes > ; > ; Energy minimizing stuff > ; > emtol = 1000.0 > emstep = 0.01 > Is it possible this could be related to insufficient memory allocation ? > How demanding is this PME calculation ? Not likely a memory problem. It could be a compiler issue but we need more info! Where does it crash? Is it reproducible? DOes the same tpr file cause a crash on another architecture (e.g. your desktop)? I installed gromacs 3.3.1 on my desktop (Pentium 4 under linux fedora core 4 and using the fftw3 fourier transform library). I used the .tpr file generated on the altix in mdrun and it worked fine. When I run that same file on the altix, it crashes every time without any iteration in the .log file: Removing pbc first time Done rmpbc Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 14580 Started Steepest Descents on node 0 Mon May 1 11:47:39 2006 PLEASE READ AND CITE THE FOLLOWING REFERENCE S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 --- Thank You --- After that the file ends. There is no other error message than segmentation fault with core dump. The compilers that are used on the altix are: C++ Version 99.0-023 -> 9.0-031 C++ Version 88.1-033 -> 8.1-036 Fortran 99.0-021 -> 9.0-032 Fortran 88.1-029 -> 8.1-033 IPP 4.1 -> 5.0 > > > > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php <>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] segmentation fault in mdrun when using PME
Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation fault and core dump at the steepest descents minimization step. However, mdrun works fine when using cutoff instead of PME. I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel Itanium 2 processors (but I'm currently using a single node, so it's not a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized for Itanium 2). the em.mdp file looks like: title = drg_trpcpp = /usr/bin/cppdefine = -DFLEX_SPCconstraints = noneintegrator = steepdt = 0.002 ; ps !nsteps = 500nstlist = 10ns_type = gridrlist = 0.9coulombtype = PMErcoulomb = 0.9rvdw = 0.9fourierspacing = 0.12fourier_nx = 0fourier_ny = 0fourier_nz = 0pme_order = 4ewald_rtol = 1e-5optimize_fft = yes;; Energy minimizing stuff;emtol = 1000.0emstep = 0.01 Is it possible this could be related to insufficient memory allocation ? How demanding is this PME calculation ? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
