Re: [gmx-users] Does current GROMACS-GPU support CMAP dihedrals in CHARMM
On 2011-5-14 0:52, zw...@cam.ac.uk wrote: Hello. I am writing to ask if current GROMACS-GPU supports CMAP dihedrals in CHARMM. We are trying to run GROMACS on GPU. It is mentioned on GROMACS website (http://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=gpu) that CMAP dihedrals in CHARMM are not support. However, we found it is supported in current OpenMM. Is this problem solved in current GROMACS-GPU version? Cheers, Zhi Hello all, I am not sure this is the suitable place for my question. Or should I post it to gmx-developers? Cheers, Zhi -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Does current GROMACS-GPU support CMAP dihedrals in CHARMM
Hi, Only OpenMM-2.0 (no CMAP) is supported in the gromacs 4.5 releases. There are no plans at the moment to support all new functionality in OpenMM-3.0. Cheers, Rossen On 5/16/11 9:06 AM, Zhi Wang wrote: On 2011-5-14 0:52, zw...@cam.ac.uk wrote: Hello. I am writing to ask if current GROMACS-GPU supports CMAP dihedrals in CHARMM. We are trying to run GROMACS on GPU. It is mentioned on GROMACS website (http://www.gromacs.org/Downloads/Installation_Instructions/GPUs?highlight=gpu) that CMAP dihedrals in CHARMM are not support. However, we found it is supported in current OpenMM. Is this problem solved in current GROMACS-GPU version? Cheers, Zhi Hello all, I am not sure this is the suitable place for my question. Or should I post it to gmx-developers? Cheers, Zhi -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
R: Re: [gmx-users] numbering of .gro file
Dear gmx-users, first let me resume my attempts on this question. 1) Using: pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top I obtained a .gro file in which the numbering of each chain correctly starts from 21 to 379 in both chains, but no chain ID is present, so I cannot distinguish residues of chain A from residues of chain B 2) Using: pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top -renum I obtained a .gro file in which the numbering of each chain starts from 1 to 359 in both chains (i.e. the second chain does not continue the numbering from 360), but no chain ID is present, so again I cannot distinguish residues of chain A from residues of chain B 3) Using: pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top -chainsep id I obtained a .gro file in which the numbering of each chain starts from 21 to 379 in both chains (i.e. the second chain does not continue the numbering from 360), but no chain ID is present, so again I cannot distinguish residues of chain A from residues of chain B. 4) Using: pdb2gmx -f my_protein.pdb -o my_protein.pdb -p my_protein.top I obtained an output .pdb file in which the numbering and the chain ID of the input .pdb file are kept (and so I can distinguish between the residues of chain A and of chain B. However, when I continue with editconf+genbox and add 22586 water molecules, I have the problem of more than residues, which is not compatible with a .pdb format, so the numbering of the residues restarts twice from zero. My question is: can I distinguish chain A and B of my protein (either with a chain ID or with a consecutive numbering of the two chains) AND have a file format compatible with more than residues using Gromacs only? Thank you very much Anna Date: Fri, 13 May 2011 09:54:38 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] numbering of .gro file To: Discussion list for GROMACS users Message-ID: <4dcd381e.1020...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear Mark, > thank you also for your suggestion, indeed using the nvt.gro file with the > sequential numbering I was able to distinguish the contributions from both > chains, instead of seeing them superimposed. > Now I have another question. I used pdb2gmx to prepare another file for > simulation (it is the same protein as above, with a mutation). The pdb file > contains two identical chains numbered starting from 21 to 379, marked with > chain ID A and B. > Using the command line: > pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top > I obtained a .gro file in which the numbering correctly starts from 21 to > 379 in both chains, but no chain ID is present. I also tried to use > -chainsep, but nothing changed. So my (last) question is: is there any way > to avoid renumbering the file, but without obtaining a superposition of > residue numbers in both subunits? In other workds: is there a possibility to > leave some form of "chain identifier" in the .gro file? Or the only way to > obtain unambiguous identification of each residue is to renumber the file? There are no chain identifiers in .gro format. If you want them, use .pdb instead. You can make use of a variety of formats for just about all the Gromacs tools; there is no requirement for .gro. If your input .pdb file has chain identifiers, so too should the output structure. -Justin -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to get angle distribution between two tyrosine stacking residues
Hello users, Can anyone tell how to calculate the normal-normal angle between two stacking tyrosine residues as a function of time. -- --- Regards, Bipin Singh -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error in kalp15 in water tutorial
To all gromacs user, I m trying the KALP15 in water tutorial, in which at the second command "grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr", i have got the following error: ERROR 1 [file dppc.itp, line 112]: No default LJ-14 types ERROR 2 [file dppc.itp, line 113]: No default LJ-14 types ERROR 3 [file dppc.itp, line 114]: No default LJ-14 types ERROR 4 [file dppc.itp, line 115]: No default LJ-14 types ERROR 5 [file dppc.itp, line 116]: No default LJ-14 types ERROR 6 [file dppc.itp, line 117]: No default LJ-14 types ERROR 7 [file dppc.itp, line 118]: No default LJ-14 types ERROR 8 [file dppc.itp, line 119]: No default LJ-14 types ERROR 9 [file dppc.itp, line 120]: No default LJ-14 types ERROR 10 [file dppc.itp, line 121]: No default LJ-14 types ERROR 11 [file dppc.itp, line 122]: No default LJ-14 types ERROR 12 [file dppc.itp, line 123]: No default LJ-14 types ERROR 13 [file dppc.itp, line 124]: No default LJ-14 types ERROR 14 [file dppc.itp, line 125]: No default LJ-14 types ERROR 15 [file dppc.itp, line 126]: No default LJ-14 types ERROR 16 [file dppc.itp, line 127]: No default LJ-14 types ERROR 17 [file dppc.itp, line 128]: No default LJ-14 types ERROR 18 [file dppc.itp, line 129]: No default LJ-14 types ERROR 19 [file dppc.itp, line 130]: No default LJ-14 types ERROR 20 [file dppc.itp, line 131]: No default LJ-14 types ERROR 21 [file dppc.itp, line 132]: No default LJ-14 types ERROR 22 [file dppc.itp, line 133]: No default LJ-14 types ERROR 23 [file dppc.itp, line 134]: No default LJ-14 types ERROR 24 [file dppc.itp, line 135]: No default LJ-14 types ERROR 25 [file dppc.itp, line 136]: No default LJ-14 types ERROR 26 [file dppc.itp, line 137]: No default LJ-14 types ERROR 27 [file dppc.itp, line 138]: No default LJ-14 types ERROR 28 [file dppc.itp, line 139]: No default LJ-14 types ERROR 29 [file dppc.itp, line 140]: No default LJ-14 types Excluding 3 bonded neighbours molecule type 'DPPC' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.5.4 Source code file: grompp.c, line: 1370 Fatal error: There were 29 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- can anybody solve this problem. thanks in advace. preeti-- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] adding new lipid into /charmm27.ff/lipids.rtp
Dear All, Hi! I 'm using Charmm-gui to generate an empty membrane pdb and toppar, i managed to get the charmm topology from toppar directory. With that, I'm trying to put additional lipid topology from charmm-gui into /charmm27.ff/lipids.rtp (gromacs4.5.4) for my empty membrane. But with pdb2gmx, it failed to recognize the residue type with the error "Residue not found in residue topology database". May i know in the rtp file format, is the spacing crucial in order for gromacs to process? thank you in advance. best regards, bing -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] reg pull code for protein ligand interaction
vidhya sankar wrote: Dear justin, Thank you for your reply, can i use pull code of umberla pullings in Protein ligand interaction. otherwise is it possible to use pull code for chain pulling ?. Yes. i need to implement pull code for a ligand of a protein because your manual pull code is applied only to peptide chain pulling. Just because a tutorial does one thing doesn't mean you can't use the principle in other systems. There are plenty of examples of protein-ligand umbrella sampling in the literature. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error in kalp15 in water tutorial
Preeti Gupta wrote: To all gromacs user, I m trying the KALP15 in water tutorial, in which at the second command "grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr", i have got the following error: ERROR 1 [file dppc.itp, line 112]: No default LJ-14 types You haven't properly constructed the necessary force field files, hence all of these atom types are going unrecognized. -Justin ERROR 2 [file dppc.itp, line 113]: No default LJ-14 types ERROR 3 [file dppc.itp, line 114]: No default LJ-14 types ERROR 4 [file dppc.itp, line 115]: No default LJ-14 types ERROR 5 [file dppc.itp, line 116]: No default LJ-14 types ERROR 6 [file dppc.itp, line 117]: No default LJ-14 types ERROR 7 [file dppc.itp, line 118]: No default LJ-14 types ERROR 8 [file dppc.itp, line 119]: No default LJ-14 types ERROR 9 [file dppc.itp, line 120]: No default LJ-14 types ERROR 10 [file dppc.itp, line 121]: No default LJ-14 types ERROR 11 [file dppc.itp, line 122]: No default LJ-14 types ERROR 12 [file dppc.itp, line 123]: No default LJ-14 types ERROR 13 [file dppc.itp, line 124]: No default LJ-14 types ERROR 14 [file dppc.itp, line 125]: No default LJ-14 types ERROR 15 [file dppc.itp, line 126]: No default LJ-14 types ERROR 16 [file dppc.itp, line 127]: No default LJ-14 types ERROR 17 [file dppc.itp, line 128]: No default LJ-14 types ERROR 18 [file dppc.itp, line 129]: No default LJ-14 types ERROR 19 [file dppc.itp, line 130]: No default LJ-14 types ERROR 20 [file dppc.itp, line 131]: No default LJ-14 types ERROR 21 [file dppc.itp, line 132]: No default LJ-14 types ERROR 22 [file dppc.itp, line 133]: No default LJ-14 types ERROR 23 [file dppc.itp, line 134]: No default LJ-14 types ERROR 24 [file dppc.itp, line 135]: No default LJ-14 types ERROR 25 [file dppc.itp, line 136]: No default LJ-14 types ERROR 26 [file dppc.itp, line 137]: No default LJ-14 types ERROR 27 [file dppc.itp, line 138]: No default LJ-14 types ERROR 28 [file dppc.itp, line 139]: No default LJ-14 types ERROR 29 [file dppc.itp, line 140]: No default LJ-14 types Excluding 3 bonded neighbours molecule type 'DPPC' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.5.4 Source code file: grompp.c, line: 1370 Fatal error: There were 29 errors in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- can anybody solve this problem. thanks in advace. preeti -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] adding new lipid into /charmm27.ff/lipids.rtp
Bing Bing wrote: Dear All, Hi! I 'm using Charmm-gui to generate an empty membrane pdb and toppar, i managed to get the charmm topology from toppar directory. With that, I'm trying to put additional lipid topology from charmm-gui into /charmm27.ff/lipids.rtp (gromacs4.5.4) for my empty membrane. But with pdb2gmx, it failed to recognize the residue type with the error "Residue not found in residue topology database". May i know in the rtp file format, is the spacing crucial in order for gromacs to process? Manual section 5.6.1. You can use the other .rtp entries in the force field as a guide. Whitespace is unimportant. Note that you may get a mess of topologies if you run pdb2gmx on a complete membrane, especially if the it's a pure membrane. pdb2gmx is intended for construction topologies from repeat units, e.g. to build proteins and other (mostly) linear polymers. If you want to use pdb2gmx, you're better off doing so an a coordinate file of a single lipid and using that as an #included topology in the system .top. Much cleaner. -Justin thank you in advance. best regards, bing -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] "Command Not Found"
Hi All, Sorry to bug you all about this - it's been mentioned a few times but I can't find an answer that seems to relate to the situation I've got. I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5, however, everytime I type the commands I get 'g_fda*: command not found'. These are present in the /usr/local/gromacs/bin directory - however when I've checked over the config.log they haven't installed. I'm not sure I understand what's happened - the installation was done by downloading followed by ./configure, make, make install, and everything else seems to be functioning fine. What is it I've missed? Can anyone shed any light on my (probably completely stupid) problem?! Thanks loads, Natalie Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] "Command Not Found"
Natalie Stephenson wrote: Hi All, Sorry to bug you all about this - it's been mentioned a few times but I can't find an answer that seems to relate to the situation I've got. I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5, however, everytime I type the commands I get 'g_fda*: command not found'. Using wildcards will not find command names. These are present in the /usr/local/gromacs/bin directory - however when I've checked over the config.log they haven't installed. I'm not sure I OK, so you have an executable installed, but it didn't install? Can you please clarify? Neither g_fdaconv or g_fdatools are standard Gromacs utilities - are they some sort of external package or add-on? -Justin understand what's happened - the installation was done by downloading followed by ./configure, make, make install, and everything else seems to be functioning fine. What is it I've missed? Can anyone shed any light on my (probably completely stupid) problem?! Thanks loads, Natalie Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: R: Re: [gmx-users] numbering of .gro file
Anna Marabotti wrote: Dear gmx-users, first let me resume my attempts on this question. 1) Using: pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top I obtained a .gro file in which the numbering of each chain correctly starts from 21 to 379 in both chains, but no chain ID is present, so I cannot distinguish residues of chain A from residues of chain B 2) Using: pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top -renum I obtained a .gro file in which the numbering of each chain starts from 1 to 359 in both chains (i.e. the second chain does not continue the numbering from 360), but no chain ID is present, so again I cannot distinguish residues of chain A from residues of chain B 3) Using: pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top -chainsep id I obtained a .gro file in which the numbering of each chain starts from 21 to 379 in both chains (i.e. the second chain does not continue the numbering from 360), but no chain ID is present, so again I cannot distinguish residues of chain A from residues of chain B. 4) Using: pdb2gmx -f my_protein.pdb -o my_protein.pdb -p my_protein.top I obtained an output .pdb file in which the numbering and the chain ID of the input .pdb file are kept (and so I can distinguish between the residues of chain A and of chain B. However, when I continue with editconf+genbox and add 22586 water molecules, I have the problem of more than residues, which is not compatible with a .pdb format, so the numbering of the residues restarts twice from zero. My question is: can I distinguish chain A and B of my protein (either with a chain ID or with a consecutive numbering of the two chains) AND have a file format compatible with more than residues using Gromacs only? Probably not. The .gro format allows for a bit more flexibility in residue numbering, but no chain identifiers; vice versa for .pdb. Careful creation of index files will allow you to circumvent both problems. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] "Command Not Found"
Sorry for the confusion - didn't mean I'd used a wildcard when typing the
commands ... just meant I get that response for both commands.
They're an add on created from a the Molecular BioMechanics group
(http://projects.eml.org/mbm/website/fda_gromacs.htm) - I've downloaded they're
software as they mention:
Installing the FDAtools package:
FDAtools depends on bio3d and SparsM. Please download the bio3d package.
A a Mac / Linux user, check that your R_LIBS variable points to the folder in
which packages should be installed (insert an export R_LIBS="..." in your
.profile / .bashrc if not previously done).
Install bio3d by executing 'R CMD INSTALL bio3d_1.0-6.tar.gz'.
Install SparseM by executing 'install.packages("SparseM")' in an R console.
Now we are ready to install FDAtools, just type 'R CMD INSTALL
FDAtools_0.9.tar.gz' on the command line.
And downloaded the 'gromacs_4.0.5_pf' that they have (FDA-Gromacs). Is it
likely to be some problem with the FDA-Gromacs package installation (the one I
mentioned below) ... or is it likely to be something else?
Thanks
Natalie
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: 16 May 2011 15:56
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] "Command Not Found"
Natalie Stephenson wrote:
> Hi All,
>
> Sorry to bug you all about this - it's been mentioned a few times but I
> can't find an answer that seems to relate to the situation I've got.
>
> I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5,
> however, everytime I type the commands I get 'g_fda*: command not found'.
>
Using wildcards will not find command names.
> These are present in the /usr/local/gromacs/bin directory - however when
> I've checked over the config.log they haven't installed. I'm not sure I
OK, so you have an executable installed, but it didn't install? Can you please
clarify? Neither g_fdaconv or g_fdatools are standard Gromacs utilities - are
they some sort of external package or add-on?
-Justin
> understand what's happened - the installation was done by downloading
> followed by ./configure, make, make install, and everything else seems
> to be functioning fine. What is it I've missed?
>
> Can anyone shed any light on my (probably completely stupid) problem?!
>
> Thanks loads,
> Natalie
>
>
> Natalie Stephenson, B.Sc
> PhD Research Associate
>
> Manchester Interdisciplinary Biocentre
> 131 Princess Street
> Manchester
> M1 7DN
> x65816
>
>
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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 it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
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 it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] "Command Not Found"
Natalie Stephenson wrote:
Sorry for the confusion - didn't mean I'd used a wildcard when typing the
commands ... just meant I get that response for both commands.
They're an add on created from a the Molecular BioMechanics group
(http://projects.eml.org/mbm/website/fda_gromacs.htm) - I've downloaded
they're software as they mention:
Installing the FDAtools package: FDAtools depends on bio3d and SparsM. Please
download the bio3d package. A a Mac / Linux user, check that your R_LIBS
variable points to the folder in which packages should be installed (insert
an export R_LIBS="..." in your .profile / .bashrc if not previously done).
Install bio3d by executing 'R CMD INSTALL bio3d_1.0-6.tar.gz'. Install
SparseM by executing 'install.packages("SparseM")' in an R console. Now we
are ready to install FDAtools, just type 'R CMD INSTALL FDAtools_0.9.tar.gz'
on the command line.
And downloaded the 'gromacs_4.0.5_pf' that they have (FDA-Gromacs). Is it
likely to be some problem with the FDA-Gromacs package installation (the one
I mentioned below) ... or is it likely to be something else?
If you're having a problem with some external package, your best bet is to
contact those developers directly. Your previous message said that you were
able to install the package and the executables were in /usr/local/gromacs/bin,
which probably just means your environment isn't configured properly:
http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation
If the installation was actually successful, this is all you should need to do,
as you would with any Gromacs installation, custom or otherwise.
-Justin
Thanks Natalie
From: gmx-users-boun...@gromacs.org
[gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul
[jalem...@vt.edu] Sent: 16 May 2011 15:56 To: Discussion list for GROMACS
users Subject: Re: [gmx-users] "Command Not Found"
Natalie Stephenson wrote:
Hi All,
Sorry to bug you all about this - it's been mentioned a few times but I
can't find an answer that seems to relate to the situation I've got.
I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5, however,
everytime I type the commands I get 'g_fda*: command not found'.
Using wildcards will not find command names.
These are present in the /usr/local/gromacs/bin directory - however when
I've checked over the config.log they haven't installed. I'm not sure I
OK, so you have an executable installed, but it didn't install? Can you
please clarify? Neither g_fdaconv or g_fdatools are standard Gromacs
utilities - are they some sort of external package or add-on?
-Justin
understand what's happened - the installation was done by downloading
followed by ./configure, make, make install, and everything else seems to
be functioning fine. What is it I've missed?
Can anyone shed any light on my (probably completely stupid) problem?!
Thanks loads, Natalie
Natalie Stephenson, B.Sc
PhD Research Associate
Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1
7DN x65816
--
Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu |
(540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
-- gmx-users mailing list
gmx-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
it to gmx-users-requ...@gromacs.org. Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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 it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] "Command Not Found"
Hi Natalie,
You're in the wrong place, and probably trying the wrong thing. The
FDAtools are not part of Gromacs and if you encounter issues with them
you should raise it with the authors. They may have a user list too.
Aside from that, the FDAtools seem to be an R package. That means that
they will offer you extended functionality within R, and not as
command line tools.
Cheers,
Tsjerk
On Mon, May 16, 2011 at 5:01 PM, Natalie Stephenson
wrote:
> Sorry for the confusion - didn't mean I'd used a wildcard when typing the
> commands ... just meant I get that response for both commands.
>
> They're an add on created from a the Molecular BioMechanics group
> (http://projects.eml.org/mbm/website/fda_gromacs.htm) - I've downloaded
> they're software as they mention:
>
> Installing the FDAtools package:
> FDAtools depends on bio3d and SparsM. Please download the bio3d package.
> A a Mac / Linux user, check that your R_LIBS variable points to the folder in
> which packages should be installed (insert an export R_LIBS="..." in your
> .profile / .bashrc if not previously done).
> Install bio3d by executing 'R CMD INSTALL bio3d_1.0-6.tar.gz'.
> Install SparseM by executing 'install.packages("SparseM")' in an R console.
> Now we are ready to install FDAtools, just type 'R CMD INSTALL
> FDAtools_0.9.tar.gz' on the command line.
>
> And downloaded the 'gromacs_4.0.5_pf' that they have (FDA-Gromacs). Is it
> likely to be some problem with the FDA-Gromacs package installation (the one
> I mentioned below) ... or is it likely to be something else?
>
> Thanks
> Natalie
>
>
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
> of Justin A. Lemkul [jalem...@vt.edu]
> Sent: 16 May 2011 15:56
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] "Command Not Found"
>
> Natalie Stephenson wrote:
>> Hi All,
>>
>> Sorry to bug you all about this - it's been mentioned a few times but I
>> can't find an answer that seems to relate to the situation I've got.
>>
>> I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5,
>> however, everytime I type the commands I get 'g_fda*: command not found'.
>>
>
> Using wildcards will not find command names.
>
>> These are present in the /usr/local/gromacs/bin directory - however when
>> I've checked over the config.log they haven't installed. I'm not sure I
>
> OK, so you have an executable installed, but it didn't install? Can you
> please
> clarify? Neither g_fdaconv or g_fdatools are standard Gromacs utilities - are
> they some sort of external package or add-on?
>
> -Justin
>
>> understand what's happened - the installation was done by downloading
>> followed by ./configure, make, make install, and everything else seems
>> to be functioning fine. What is it I've missed?
>>
>> Can anyone shed any light on my (probably completely stupid) problem?!
>>
>> Thanks loads,
>> Natalie
>>
>>
>> Natalie Stephenson, B.Sc
>> PhD Research Associate
>>
>> Manchester Interdisciplinary Biocentre
>> 131 Princess Street
>> Manchester
>> M1 7DN
>> x65816
>>
>>
>
> --
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> --
> gmx-users mailing list gmx-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 it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing list gmx-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 it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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 it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] "Command Not Found"
Thanks loads ... that worked perfectly!! Environment configured!! :D
xxx
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: 16 May 2011 16:09
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] "Command Not Found"
Natalie Stephenson wrote:
> Sorry for the confusion - didn't mean I'd used a wildcard when typing the
> commands ... just meant I get that response for both commands.
>
> They're an add on created from a the Molecular BioMechanics group
> (http://projects.eml.org/mbm/website/fda_gromacs.htm) - I've downloaded
> they're software as they mention:
>
> Installing the FDAtools package: FDAtools depends on bio3d and SparsM. Please
> download the bio3d package. A a Mac / Linux user, check that your R_LIBS
> variable points to the folder in which packages should be installed (insert
> an export R_LIBS="..." in your .profile / .bashrc if not previously done).
> Install bio3d by executing 'R CMD INSTALL bio3d_1.0-6.tar.gz'. Install
> SparseM by executing 'install.packages("SparseM")' in an R console. Now we
> are ready to install FDAtools, just type 'R CMD INSTALL FDAtools_0.9.tar.gz'
> on the command line.
>
> And downloaded the 'gromacs_4.0.5_pf' that they have (FDA-Gromacs). Is it
> likely to be some problem with the FDA-Gromacs package installation (the one
> I mentioned below) ... or is it likely to be something else?
>
If you're having a problem with some external package, your best bet is to
contact those developers directly. Your previous message said that you were
able to install the package and the executables were in /usr/local/gromacs/bin,
which probably just means your environment isn't configured properly:
http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation
If the installation was actually successful, this is all you should need to do,
as you would with any Gromacs installation, custom or otherwise.
-Justin
> Thanks Natalie
>
> From: gmx-users-boun...@gromacs.org
> [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul
> [jalem...@vt.edu] Sent: 16 May 2011 15:56 To: Discussion list for GROMACS
> users Subject: Re: [gmx-users] "Command Not Found"
>
> Natalie Stephenson wrote:
>> Hi All,
>>
>> Sorry to bug you all about this - it's been mentioned a few times but I
>> can't find an answer that seems to relate to the situation I've got.
>>
>> I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5, however,
>> everytime I type the commands I get 'g_fda*: command not found'.
>>
>
> Using wildcards will not find command names.
>
>> These are present in the /usr/local/gromacs/bin directory - however when
>> I've checked over the config.log they haven't installed. I'm not sure I
>
> OK, so you have an executable installed, but it didn't install? Can you
> please clarify? Neither g_fdaconv or g_fdatools are standard Gromacs
> utilities - are they some sort of external package or add-on?
>
> -Justin
>
>> understand what's happened - the installation was done by downloading
>> followed by ./configure, make, make install, and everything else seems to
>> be functioning fine. What is it I've missed?
>>
>> Can anyone shed any light on my (probably completely stupid) problem?!
>>
>> Thanks loads, Natalie
>>
>> Natalie Stephenson, B.Sc
>> PhD Research Associate
>>
>> Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1
>> 7DN x65816
>>
>
> --
>
> Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee
> Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu |
> (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> -- gmx-users mailing list
> gmx-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
> it to gmx-users-requ...@gromacs.org. Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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 it to gmx-users-requ...
[gmx-users] g_energy
Hello, the g_energy tool in Gromacs 4.0.7 provides calculation of viscosity (-vis) and surface tension (-o surften): a) Both, the shear and bulk viscosity are calculated with -vis tool. What are the equations for calculating them? In the manual, there is only the equation for the shear viscosity. Are these values reliable? b) How is the surface tension calculated, is it also a reliable method? Regards, Thomas-- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] QMMM+NMA
Hi Gmxers, I am wondering if NMA has been introduced into QMMM part of gromacs. I am trying to get vibrational frequencies of proteins by normal mode analysis (NMA) in the framework of QMMM. Thanks, Yao -- 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 it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] compilation of g_hbond after bugfix
Hello,
I want to compile the source code gmx_hbond.c after the below
mentioned bugfix, I have already installed gromacs 4.5.3, how can I
compile only gmx_hbond.c in already installed
gromacs 4.5.3.
>Hi,
>There have been reports about inconsistencies between older (<= 4.0.7?) and
>newer versions of g_hbond, where the older seem to have been more reliable. I
>found and killed the bug >that caused the newer versions to miscount the
>hbonds. Checkout release-4-5-patches to get the bugfix, or patch it yourself
>by commenting out line 1497, which reads "return hbNo;":
> if (bBox){
>if (d>a && bMerge && (bContact || isInterchangable(hb, d, a, grpd, grpa))) {
>/* acceptor is also a donor a\
>nd vice versa? */
>/* return hbNo; */
>daSwap = TRUE; /* If so, then their history should be filed with donor and
>acceptor swapped. */
> }
>Simple as that
--
---
Thanks & Regards,
Bipin Singh
--
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 it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] compilation of g_hbond after bugfix
On 17/05/2011 3:40 PM, bipin singh wrote:
Hello,
I want to compile the source code gmx_hbond.c after the below
mentioned bugfix, I have already installed gromacs 4.5.3, how can I
compile only gmx_hbond.c in already installed
gromacs 4.5.3.
If you've built using configure, then there is no way to do this. Just
do a normal "make install" and if you have modified the source file,
make will work out what to do. You may wish to rename the old executable
before you do this, so that you can still access both versions.
If you've built using CMake, then make g_hbond should work.
Mark
Hi,
There have been reports about inconsistencies between older (<= 4.0.7?) and newer versions
of g_hbond, where the older seem to have been more reliable. I found and killed the bug>that
caused the newer versions to miscount the hbonds. Checkout release-4-5-patches to get the
bugfix, or patch it yourself by commenting out line 1497, which reads "return hbNo;":
if (bBox){
if (d>a&& bMerge&& (bContact || isInterchangable(hb, d, a, grpd, grpa))) { /*
acceptor is also a donor a\
nd vice versa? */
/* return hbNo; */
daSwap = TRUE; /* If so, then their history should be filed with donor and
acceptor swapped. */
}
Simple as that
--
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 it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
