[gmx-users] compiling gromacs-3.3.1 on itanium2 with icc and ifort
I had trouble compiling gromacs-3.3.1 parallel (but not serial) on itanium2 until I found the following post: http://www.gromacs.org/pipermail/gmx-users/2004-February/009171.html And that solution was good... I now have a functional executable. To clarify, the solution was to do this: export CFLAGS=-nocpprt before compiling gromacs. Note also that I use a compilation script and when I put this in my compilation script it did not have any effect. I had to do it from the command line before running the script for it to work. I posted this for 2 reasons: 1) to clarify the solution for those who will compile in the future. 2) to suggest that this gets incorporated into the ./configure script for the future. $ cc --version icc (ICC) 9.1 20061105 Copyright (C) 1985-2006 Intel Corporation. All rights reserved. $ f77 --version ifort (IFORT) 9.1 20061105 Copyright (C) 1985-2006 Intel Corporation. All rights reserved. Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp
himanshu khandelia wrote: Sorry, there was a little mistake in the reported output of grompp in my previous email. It should be as follows: ## Warning: atom names in protein.top and final.gro don't match (CD2 - HD1) Warning: atom names in protein.top and final.gro don't match (CE1 - CD2) Warning: atom names in protein.top and final.gro don't match (NE2 - CE1) Warning: atom names in protein.top and final.gro don't match (HE2 - NE2) WARNING 2 [file protein.top, line 35]: 4 non-matching atom names atom names from protein.top will be used atom names from final.gro will be ignored pdb2gmx reorders atoms according to the order in the rtp file. You should not ignore those warnings, because you ill have a twisted sidechain. ## On Nov 30, 2007 3:30 PM, himanshu khandelia [EMAIL PROTECTED] wrote: Hi Folks, I am not being able to debug a little problem. I hope someone will be able to point out the mistake. Here is what I am trying to do: I need to mutate a SER to a GLU residue in a protein. However, after mutation (and making a new topology), when I run grompp, I get the following error: ## processing coordinates... Warning: atom names in protein.top and p.gro don't match (CD2 - HD1) Warning: atom names in protein.top and p.gro don't match (CE1 - CD2) Warning: atom names in protein.top and p.gro don't match (NE2 - CE1) Warning: atom names in protein.top and p.gro don't match (HE2 - NE2) WARNING 2 [file protein.top, line 35]: 4 non-matching atom names atom names from protein.top will be used atom names from final.gro will be ignored ## So, the order or names of atoms do not correspond correctly any more. I cannot find out why this is the case. Here are the steps that I used to make the mutation: ## 1. Convert the initial structure (init.gro) to a pdb (init.pdb) using editconf 2. Pull out coordinates of the SER from init.pdb and change residue name from SER to GLU. Lets call this file residue-to-be-mutated.pdb 3. Rename the following atoms: (a) OG to CG (b) HG to CD in residue-to-be-mutated.pdb 4. Guess remaining coordinates (for the 2 oxygen atoms on the carboxyl group) in some external software 5. plug in the guessed coordinates into residue-to-be-mutated.pdb 6. Removed the coordinates of SER from init.pdb, and replaced them by coordinates in residue-to-be-mutated.pdb. Note that because of the insertion of two extra atoms, the numbering of atoms in the pdb file is not continuous any more. 7. Convert the resulting pdb file into .gro format using editconf. Final output is final.gro, which should have continuous numbering of atom numbers. 8. Then I also make a new protein topology using pdb2gmx. ## Any suggestions, anyone ? - The number of atoms in the initial and final .gro files differ by two, which is the same as the difference in the number of atoms between a SER and a GLU amino acid ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Double precision test failure
Berk Hess wrote: Ah, this could be the issue. Depending on how you configure the double precision binaries could have the same names as the single precision ones, or they could have _d appended. I guess the test scripts can not figure out what they should use, but currently they apparently request the _d appended names. That's correct. In addition I think that we should start distributing packages that contain both single and double precision binaries. -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Writing initial coordinates to trajectory files
Berk Hess wrote:
The initial coordinates are written immediately to the trr file,
although the file system might buffer data, you so could have to wait
until some more frames have been written.
Thanks, I see that now. It seems that somewhere between grompp and
mdrun's initial trajectory output, my initial coordinates did change
ever so slightly:
after_em.gro:
1LYSH N1 2.105 0.744 2.070
1LYSHH12 2.056 0.668 2.027
1LYSHH23 2.190 0.761 2.021
full.trr:
natoms= 9035 step= 0 time=0.000e+00 lambda= 0
...
x[0]={ 2.10518e+00, 7.43687e-01, 2.07004e+00}
x[1]={ 2.05600e+00, 6.68002e-01, 2.02700e+00}
x[2]={ 2.19043e+00, 7.61087e-01, 2.02075e+00}
But step 0 coordinates are output as you said, thanks.
--Brian.
--
Brian Helfrich
www.nanorex.com
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[gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp
Sorry, there was a little mistake in the reported output of grompp in my previous email. It should be as follows: ## Warning: atom names in protein.top and final.gro don't match (CD2 - HD1) Warning: atom names in protein.top and final.gro don't match (CE1 - CD2) Warning: atom names in protein.top and final.gro don't match (NE2 - CE1) Warning: atom names in protein.top and final.gro don't match (HE2 - NE2) WARNING 2 [file protein.top, line 35]: 4 non-matching atom names atom names from protein.top will be used atom names from final.gro will be ignored ## On Nov 30, 2007 3:30 PM, himanshu khandelia [EMAIL PROTECTED] wrote: Hi Folks, I am not being able to debug a little problem. I hope someone will be able to point out the mistake. Here is what I am trying to do: I need to mutate a SER to a GLU residue in a protein. However, after mutation (and making a new topology), when I run grompp, I get the following error: ## processing coordinates... Warning: atom names in protein.top and p.gro don't match (CD2 - HD1) Warning: atom names in protein.top and p.gro don't match (CE1 - CD2) Warning: atom names in protein.top and p.gro don't match (NE2 - CE1) Warning: atom names in protein.top and p.gro don't match (HE2 - NE2) WARNING 2 [file protein.top, line 35]: 4 non-matching atom names atom names from protein.top will be used atom names from final.gro will be ignored ## So, the order or names of atoms do not correspond correctly any more. I cannot find out why this is the case. Here are the steps that I used to make the mutation: ## 1. Convert the initial structure (init.gro) to a pdb (init.pdb) using editconf 2. Pull out coordinates of the SER from init.pdb and change residue name from SER to GLU. Lets call this file residue-to-be-mutated.pdb 3. Rename the following atoms: (a) OG to CG (b) HG to CD in residue-to-be-mutated.pdb 4. Guess remaining coordinates (for the 2 oxygen atoms on the carboxyl group) in some external software 5. plug in the guessed coordinates into residue-to-be-mutated.pdb 6. Removed the coordinates of SER from init.pdb, and replaced them by coordinates in residue-to-be-mutated.pdb. Note that because of the insertion of two extra atoms, the numbering of atoms in the pdb file is not continuous any more. 7. Convert the resulting pdb file into .gro format using editconf. Final output is final.gro, which should have continuous numbering of atom numbers. 8. Then I also make a new protein topology using pdb2gmx. ## Any suggestions, anyone ? - The number of atoms in the initial and final .gro files differ by two, which is the same as the difference in the number of atoms between a SER and a GLU amino acid ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Writing initial coordinates to trajectory files
I don't understand what it is you want. The initial coordinates are written immediately to the trr file, although the file system might buffer data, you so could have to wait until some more frames have been written. But the initial coordinates are the ones you used to generate the tpr file, so I don't see why you would want those. editconf -f topol.tpr would also give you those coordinates in gro or pdb format. Berk. From: Brian Helfrich [EMAIL PROTECTED] Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] Writing initial coordinates to trajectory files Date: Fri, 30 Nov 2007 10:43:28 -0500 Hello, Is there a setting, or some standard way to write out the initial coordinates of a system to the trajectory file instead of it waiting nstxout steps? Thanks very much, --Brian. PS. I sent this a couple days ago originally - must have gotten lost. Apologies if both make it through. -- Brian Helfrich www.nanorex.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Recover velocity from trr file and coordinates from xtc file
Thank you for your help. However, I can't understand how to generate gro file from trr and xtc files. I'm sorry. I'm a beginner. Would you let me know exact command? or where can I find? Again, I saved *velocity only in trr* file, and I have xtc file (only coordinates). I have edr file also. I found the following to make the restart file (gro file). tpbconv -s eq5.tpr -f eq5.trr -e eq5.edr -o eq6.tpr -time 6870.000 Since I have velocity only in the trr file, I can't apply this. Any idea? On Nov 29, 2007 11:17 AM, Alan Dodd [EMAIL PROTECTED] wrote: http://wiki.gromacs.org/index.php/Doing_Restarts You can make a gro with what you have. You *may* be able to continue your run properly. Read the above link. - Original Message From: Myunggi Yi [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Thursday, November 29, 2007 4:06:06 PM Subject: [gmx-users] Recover velocity from trr file and coordinates from xtc file Dear Gmx users, Can I make a gro file (restart file) from trr (I saved only velocities) and xtc file (which has the coordinates)? If I can, how can I do this job? I'm a beginner. Have a nice day. -- Best wishes, MYUNGGI YI == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- Best wishes, MYUNGGI YI == KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Replica Exchange MD using Gromacs
Dear All, I am trying REMD for the first time using Gromacs. But I am not finding any much helpful material regarding the replica exchange using Gromacs. Can anyone who has done REMD please let me know about any good tutorial where I can understand the way this replica exchange work in gromacs and the right protocol to do so.. Thanks a lot in advance.. Regards, Monika CCNSB, IIIT, Hyderabad. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] Replica Exchange MD using Gromacs
Hi Monica, I had not found a detailed tutorial about it; however, you can search for papers in which the simulations are performed via REMD.This will be helpful. Ozge. -Original Message- From: Monika Sharma [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 30 Nov 2007 17:04:07 +0530 (IST) Subject: [gmx-users] Replica Exchange MD using Gromacs Dear All, I am trying REMD for the first time using Gromacs. But I am not finding any much helpful material regarding the replica exchange using Gromacs. Can anyone who has done REMD please let me know about any good tutorial where I can understand the way this replica exchange work in gromacs and the right protocol to do so.. Thanks a lot in advance.. Regards, Monika CCNSB, IIIT, Hyderabad. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with S-S bond
Hi Tsjerk, Thanks a lot. I tried writing a new message but it was bouncing back to me and I wrote to the administrator, and was suggested to register with GMX,which I already have done. Finally it worked when I replied for a previous message. However, sorry for the inconvenience, it will not happen again. Thanks, Blaise - Original Message From: Tsjerk Wassenaar [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, November 29, 2007 11:54:43 PM Subject: Re: [gmx-users] Problem with S-S bond Hi Blaise, Disulfide bonds are only made when two Cys-S atoms are within 0.2 +/- 0.02 nm from each other. This distance is in the file specbond.dat. You can search the archives for how to make the bond. Also, please start a new thread rather than replying to a message. Now there's debris unrelated to your question, which is a bit annoying. Cheers, Tsjerk On Nov 30, 2007 12:41 AM, Blaise Costa [EMAIL PROTECTED] wrote: Hello Gromacs users, I have docked an antagonist into the agonist bound conformation and doing MDS to get the antagonist bound conformation after several nS simulation. Therefore expected that the protein might undergo big conformational changes, and running the simulation in Unconstrained Start = Yes . While starting the simulation the S atoms were close enough (3A) to make the disulphide bond. Now, after 1.5 nS, noticed that it is deviated for more than 6.5A, therefore no way to make the bond. Is there any way that I can give constraint for these bonds and can I restart the program from last point? I gave -SS command during pdb2gmx, believed that gromacs will keep the S atoms close enough to make the S-S bond. I am using Gromacs version 3.3.1! Many thanks in advance! Blaise - Original Message From: David van der Spoel [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, November 29, 2007 12:29:57 PM Subject: Re: [gmx-users] Double precision test failure Chris Snook wrote: I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 2.16GHz Core 2 Duo processor. I have downloaded and installed the v 3.3.2 binaries of gromacs for this OS and run the test program. The single precision tests run OK. But the double precision tests completely fail with the following output (partial): No topol.tpr file in angles1. grompp failed FAILED. Check files in angles1 No topol.tpr file in angles125. grompp failed FAILED. Check files in angles125 No topol.tpr file in bham. grompp failed FAILED. Check files in bham etc No topol.tpr file in kernel334. grompp failed FAILED. Check files in kernel334 63 out of 63 kernel tests FAILED readline() on closed filehandle PIPE at ./gmxtest.pl line 353. etc I've checked the archives and the manual and haven't seen anything relevant to this. Any help would be appreciated. did you source GMXRC? Regards Chris ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [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 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -Inline Attachment Follows- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use
[gmx-users] GTP topology file for ffG43a1
Dear all, I have now prepared what I think are the necessary lines for entry into the ffG43a1.rtp file for GTP, however I was wanting a quick way to test what I have done. Again I am open to suggestions. Specifically I want to ensure that I have added sufficient bonds and angles for the molecule and that I have not defined any of the parameters more than once. I am quite happy to send on my files, if someone would like to help, basically my approach has been to cannibalise the ATP, AED and GUA files. Is there a simple way to produce a .gro or .pdb file from my altered ffG43a1.rtp? Cheers, Bryn ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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] GTP topology file for ffG43a1
Quoting Robert Fenwick [EMAIL PROTECTED]: Dear all, I have now prepared what I think are the necessary lines for entry into the ffG43a1.rtp file for GTP, however I was wanting a quick way to test what I have done. Again I am open to suggestions. Specifically I want to ensure that I have added sufficient bonds and angles for the molecule and that I have not defined any of the parameters more than once. I am quite happy to send on my files, if someone would like to help, basically my approach has been to cannibalise the ATP, AED and GUA files. Is there a simple way to produce a .gro or .pdb file from my altered ffG43a1.rtp? I don't think you can make a structure from just an .rtp entry, but you could always draw the molecule with PRODRG to get the structure file, and then make adjust the atom names such that are the same as those in the .rtp, and proceed from there. -Justin Cheers, Bryn ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
