Re: [gmx-users] PDB and GRO files

[Mark Abraham]

Jim Kress wrote:
Try Openbabel.  


http://openbabel.org/wiki/Main_Page

It intercoverts most file types so, you could build your molecule with any
of the 3D model builders that serve as front ends to Quantum Chemistry
programs.  Export it as an XYZ file and then use Openbabel to convert it to
a pdb format.  Some will even export pdb formatted files.

For that matter, you could use ArgusLab to build your protein and/ or import
it from a known pdb file database.  If you choose to build your protein, it
will export it in a pdb format.  If you download one from a database,
obviously you can save it in a pdb format.

ArgusLab is also specifically designed to make building proteins simpler
(not simple - just simpler) with a built-in library of amino acids in
fragment forms that can be connected to create the protein of your choice
along with side chain fragments, solvation species, etc.

http://www.arguslab.com/

Highly recommended.


Wikified, thanks. 
http://oldwiki.gromacs.org/index.php/Coordinate_File#Sources


Mark
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Re: [gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU

[Mark Abraham]

Jim Kress wrote:
 > you do compile and experiment suitably. For GROMACS, a 
straight configure && make install is rather unlikely to be 
suitable, these days.


Why?


In most situations for production calculations you'd want an MPI version 
of mdrun. You might want shared libraries if disk space is an issue. If 
your processor lacks optimized kernels you will want to try the FORTRAN 
ones. You might need to configure for FFTW2.x. You might need a 
double-precision version. When GROMACS 4.1 comes out, you'll want to 
choose threading or not.


Mark
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RE: [gmx-users] Zn parameterization

[Jim Kress]

Probably because +2 is by far the most common oxidation state for Zn.

Jim 

> -Original Message-
> From: gmx-users-boun...@gromacs.org 
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham
> Sent: Wednesday, July 22, 2009 10:00 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Zn parameterization
> 
> Marc Charendoff wrote:
> > Hello,
> > 
> >I am curious - is there anyway to see what 
> assumptions were made when parameterizing the Zn 2+ ion? Was 
> it tetrahedrally or octahedrally coordinated? With waters 
> only or with imidazoles? Do the different force fields make 
> different assumptions?  Guidance appreciated.
> 
> Without even knowing the force field to which you were 
> referring, we can't say anything other than to refer you to 
> the primary literature for that force field.
> 
> Mark
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RE: [gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU

[Jim Kress]

 > you do compile and experiment suitably. For GROMACS, a 
> straight configure && make install is rather unlikely to be 
> suitable, these days.

Why?

Jim

> -Original Message-
> From: gmx-users-boun...@gromacs.org 
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham
> Sent: Wednesday, July 22, 2009 3:45 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Re: comparison of gromacs in CENTOS 
> and UBUNTU
> 
> Alexandre Suman de Araujo wrote:
> > Obviously the HD space has nothing to do with GMX 
> performance (unless 
> > it is full, of course), but the use of Ubuntu precompiled 
> packages can 
> > affect drastically the GMX performance, especially if you are also 
> > using pre-compiled MPI library package.
> > 
> > An important rule when you are interested in High 
> Performance Computing: 
> > Compile
> > ALL your softwares (the last REALLY stable version) using GOOD 
> > compilers (GCC is fine, but if you have access to Intel or Portland 
> > ones is better).
> > 
> > This rule is highly recommended ALSO to your linux kernel.
> > 
> > Never leave the important and easy work of compile your important 
> > programs with unknown people!
> 
> Caveat that you need to be reasonably competent at compiling 
> software at least for your machine and those pieces of 
> software in order to be assured you're not doing a worse job 
> then those maligned nameless people. Acquiring the necessary 
> expertise is something of a hit-and-miss process, and so I 
> would leave things like MPI and FFTW libraries and kernels 
> alone to the supervision of people who think they know about 
> them. Perhaps one could try some different versions of 
> libraries to find the best one, or make some inquiries about 
> the experience of the person who compiled the library to help judge.
> 
> Then also, consult the available documentation for the things 
> you do compile and experiment suitably. For GROMACS, a 
> straight configure && make install is rather unlikely to be 
> suitable, these days.
> 
> Mark
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RE: [gmx-users] PDB and GRO files

[Jim Kress]

Try Openbabel.  

http://openbabel.org/wiki/Main_Page

It intercoverts most file types so, you could build your molecule with any
of the 3D model builders that serve as front ends to Quantum Chemistry
programs.  Export it as an XYZ file and then use Openbabel to convert it to
a pdb format.  Some will even export pdb formatted files.

For that matter, you could use ArgusLab to build your protein and/ or import
it from a known pdb file database.  If you choose to build your protein, it
will export it in a pdb format.  If you download one from a database,
obviously you can save it in a pdb format.

ArgusLab is also specifically designed to make building proteins simpler
(not simple - just simpler) with a built-in library of amino acids in
fragment forms that can be connected to create the protein of your choice
along with side chain fragments, solvation species, etc.

http://www.arguslab.com/

Highly recommended.

Jim

> -Original Message-
> From: gmx-users-boun...@gromacs.org 
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
> Sent: Tuesday, July 21, 2009 6:16 PM
> To: Gromacs Users' List
> Subject: Re: [gmx-users] PDB and GRO files
> 
> 
> 
> Jamie Seyed wrote:
> > Hi Justin,
> >  
> > On Tue, Jul 21, 2009 at 5:04 PM, Justin A. Lemkul  > > wrote:
> > 
> > 
> > 
> > Jamie Seyed wrote:
> > 
> > Hi,
> > Thanks for your comments. But I do not know how to 
> get (or make)
> > the pdb file if it is not made (let say for a new 
> system). Are
> > you using special software to do that to make a pdb 
> or gro file,
> > before starting the simulation?
> > 
> > 
> > That's going to depend entirely upon what that system 
> is.  Building
> > a protein or peptide is not so trivial.  Building a 
> small molecule
> > is fairly straightforward using programs like PRODRG (online) or
> > xLeap (part of AmberTools).
> > 
> > That said, if your goal is to simulate some arbitrary small
> > molecules, the previous advice of using pdb2gmx will 
> not apply.  You
> > will have to build the topologies yourself. 
> > 
> >  
> > Is the result of using these programs a pdb file or gro.. would 
> > you please explain a little bit?
> 
> The documentation of each program will explain the output formats.
> 
> > The systems that I want to simulate are fullerene and CNT. 
> But before
> 
> Then neither PRODRG nor xLeap will be of use to you; xLeap 
> might work, but it's probably about the hardest way to do it :)
> 
> > that I will simulate a box of water, spce. In this case is it ok to 
> > use spc216.pdb (??) or I should use the programs you mentioned?
> 
> Use spc216.gro - it's a pre-equilibrated box that is suitable 
> for use in further simulations.
> 
> > Sorry for these simple questions..
> > 
> > 
> > 
> > Another thing: It is not possible for me to open 
> some web-pages
> > that users are referring to (some of them are 
> crucial to get the
> > answer)!! Did you face with the same problem or there is new
> > web-address for them??
> >  
> > 
> > 
> > If you cite some examples, maybe someone can point you 
> in the right
> > direction. The Gromacs webpage is currently migrating 
> to a new site;
> > old webpages can be accessed by appending "old" to the URL, i.e.
> > http://oldwww.gromacs.org  
> is the old
> > home page.
> > 
> >  
> > For example I checked 
> http://www.gromacs.org/WIKI-import/PRODRG as you 
> > mentioned, but I can not open links on the page. All of them (check 
> > force field for example) can not open with like this message "Site 
> > settings could not be loaded"...
> 
> Use Google to search for PRODRG; the link in the wiki article 
> is incorrect.  But as I said above, for your purposes, PRODRG 
> is not useful.
> 
> > Is it the page I should use to get a pdb file for my 
> system?? I really 
> > appreciate if you let me know the exact web-address to use 
> PRODRG or 
> > xLeap (?).
> >  
> 
> Use Google to find things.
> 
> This page is probably where you will want to start:
> 
> http://www.gromacs.org/WIKI-import/Carbon_Nanotube
> 
> -Justin
> 
> > Thanks a lot,
> > Jamie
> >  
> > 
> > 
> > 
> > -Justin
> > 
> > Thanks for your help,
> > Jamie
> > 
> > On Tue, Jul 21, 2009 at 4:17 PM, Rodrigo faccioli
> >  > 
> >  > >> wrote:
> > 
> >Hi,
> > 
> >If I understood your question, do you want to 
> know how can
> > you start
> >a simulation? So, if I'm correct I recommend this link
> >
> http://www.gromacs.org/WIKI-import/Main_Page/Beginners to you. In
> >this link, there is flowsheet file which is the 
> flowchart to
> > Gromacs
> >simulati

RE: [gmx-users] error in ffG43a1p force field

[jimkress_58]

He didn't have a CC: to smit...@cancer.org.uk so he probably felt he had to
resubmit the question,  LOL.

Jim

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: Friday, July 24, 2009 7:22 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] error in ffG43a1p force field



Thamu wrote:
> Hi,
> 
> i am trying to run md for protein-peptide complex. the peptide has
> phosphorylated tyrosine.
> 
> i got the following error when i run pdb2gmx
> 
> Fatal error:
> Error in hdb file ffG43a1p.hdb:
> Wrong number of control atoms (2 iso 3) on line:

So, did you follow Mark's advice and read section 5.6.2?  Repeating a
question 
without reference to previous help is usually a fast way to get ignored. 
Demonstrate that you are willing to help yourself before you expect to get
more 
free help :)

This is indeed a formatting issue.  The ffG43a1p force field was designed
for 
use with Gromacs-3.1.x, when formatting of these files was slightly
different. 
They are quite easy to fix, if you read the manual.

-Justin

>11N-CCA
> 
> I also tried with phosphoserine, i got the same error as for 
> phosphotyrosine.
> I am using gromacs-4.0.2.
> 
> 
> I would greatly appreciate if some one help me to solve this error.
> 
> Thanking you,
> 
> Yours sincerely,
> Thamu
> 
> 
> 
> 
> ___
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-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: Problem compiling gromacs-4.0.5 against mvapich2-1.4rc1

[chris . neale]

Found it.

Jerry got the solution here:  
http://mail.cse.ohio-state.edu/pipermail/mvapich-discuss/2009-July/002403.html


Thanks Jerry,
Chris.

Quoting chris.ne...@utoronto.ca:


Hi Jerry,

did you have any luck solving this? I have run into the same problem
compiling gromacs-4.0.5 with MVAPICH2-1.4rc1 using the intel compiler.
I was able to successfully compile gromacs-4.0.5 using openmpi-1.3.2
and the intel compiler. In both cases, the MPI libraries were compiled
using the intel compiler v11.0.081.

make errors out with:

...
mpicc -DHAVE_CONFIG_H -I. -I../../src  -I../../include
-DGMXLIBDIR=\"/scratch/cneale/exe/intel/gromacs-4.0.5/exec/share/top\"
-I/scratch/cneale/exe/intel/fftw-3.1.2/exec/include
-I/scinet/gpc/mpi/mvapich2/1.4rc1-3378_intel-v11.0_ofed/include
-I/scinet/gpc/mpi/mvapich2/1.4rc1-3378_intel-v11.0_ofed/lib
-I/usr/local/include  -O3 -tpp7 -axW -ip -w -funroll-all-loops
-std=gnu99 -MT grompp.o -MD -MP -MF .deps/grompp.Tpo -c -o grompp.o
grompp.c
grompp.c(983): (col. 5) remark: LOOP WAS VECTORIZED.
mv -f .deps/grompp.Tpo .deps/grompp.Po
/bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3 -tpp7 -axW -ip
-w -funroll-all-loops -std=gnu99
-L/scratch/cneale/exe/intel/fftw-3.1.2/exec/lib   -o grompp grompp.o
libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la
-lnsl -lfftw3f
mpicc -O3 -tpp7 -axW -ip -w -funroll-all-loops -std=gnu99 -o grompp
grompp.o  -L/scratch/cneale/exe/intel/fftw-3.1.2/exec/lib
./.libs/libgmxpreprocess_mpi.a ../mdlib/.libs/libmd_mpi.a
/scratch/cneale/exe/intel/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a
../gmxlib/.libs/libgmx_mpi.a -lnsl
/scratch/cneale/exe/intel/fftw-3.1.2/exec/lib/libfftw3f.a -lm
/scinet/gpc/mpi/mvapich2/1.4rc1-3378_intel-v11.0_ofed/lib/libmpich.a(ibv_channel_manager.o):(.bss+0x18): multiple definition   
of

`debug'
/scratch/cneale/exe/intel/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a(gmx_fatal.o):(.bss+0x530): first   
defined

here
make[3]: *** [grompp] Error 1
make[3]: Leaving directory
`/scratch/cneale/exe/intel/gromacs-4.0.5/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/scratch/cneale/exe/intel/gromacs-4.0.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/scratch/cneale/exe/intel/gromacs-4.0.5/src'
make: *** [all-recursive] Error 1


could this 'debug' be the one int calls like this? I at first looked
for a debug() function but didn't find any.

$ grep debug src/gmxlib/*.c
...
main.c:  if (debug) {
main.c:fprintf(debug,"This is simulation %d",cr->ms->sim);
main.c:  fprintf(debug,", local number of nodes %d, local nodeid %d",
main.c:fprintf(debug,"\n\n");
...

Thanks,
Chris

#3

-- original message --

Hello all,

I have built MVAPICH2-1.4rc1 with Infiniband support on a CentOS 5.3 box and
am trying to build gromacs-4.0.5 with MPI support.

make is failing with the following error message:

mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -std=gnu99 -o grompp grompp.o
./.libs/libgmxpreprocess_mpi.a -L/usr/lib64 ../mdlib/.libs/libmd_mpi.a
/<...snip..>/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a
../gmxlib/.libs/libgmx_mpi.a -lxml2 -lnsl -lfftw3f -lm -lX11

/usr/local/lib/libmpich.a(ibv_channel_manager.o):(.bss+0x10): multiple
definition of `debug'
<..snip..>/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a(gmx_fatal.o):(.bss+0x0):
first defined here
collect2: ld returned 1 exit status
make[3]: *** [grompp] Error 1

It looks like 'debug' is conflicting in both MVAPICH2 and in Gromacs.

Any suggestions?

Thanks,

Jerry.
Research Systems Administrator
SBGrid







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[gmx-users] Problem compiling gromacs-4.0.5 against mvapich2-1.4rc1

[chris . neale]

Hi Jerry,

did you have any luck solving this? I have run into the same problem  
compiling gromacs-4.0.5 with MVAPICH2-1.4rc1 using the intel compiler.  
I was able to successfully compile gromacs-4.0.5 using openmpi-1.3.2  
and the intel compiler. In both cases, the MPI libraries were compiled  
using the intel compiler v11.0.081.


make errors out with:

...
mpicc -DHAVE_CONFIG_H -I. -I../../src  -I../../include  
-DGMXLIBDIR=\"/scratch/cneale/exe/intel/gromacs-4.0.5/exec/share/top\"  
-I/scratch/cneale/exe/intel/fftw-3.1.2/exec/include  
-I/scinet/gpc/mpi/mvapich2/1.4rc1-3378_intel-v11.0_ofed/include  
-I/scinet/gpc/mpi/mvapich2/1.4rc1-3378_intel-v11.0_ofed/lib  
-I/usr/local/include  -O3 -tpp7 -axW -ip -w -funroll-all-loops  
-std=gnu99 -MT grompp.o -MD -MP -MF .deps/grompp.Tpo -c -o grompp.o  
grompp.c

grompp.c(983): (col. 5) remark: LOOP WAS VECTORIZED.
mv -f .deps/grompp.Tpo .deps/grompp.Po
/bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3 -tpp7 -axW -ip  
-w -funroll-all-loops -std=gnu99   
-L/scratch/cneale/exe/intel/fftw-3.1.2/exec/lib   -o grompp grompp.o  
libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la   
-lnsl -lfftw3f
mpicc -O3 -tpp7 -axW -ip -w -funroll-all-loops -std=gnu99 -o grompp  
grompp.o  -L/scratch/cneale/exe/intel/fftw-3.1.2/exec/lib  
./.libs/libgmxpreprocess_mpi.a ../mdlib/.libs/libmd_mpi.a  
/scratch/cneale/exe/intel/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a  
../gmxlib/.libs/libgmx_mpi.a -lnsl  
/scratch/cneale/exe/intel/fftw-3.1.2/exec/lib/libfftw3f.a -lm
/scinet/gpc/mpi/mvapich2/1.4rc1-3378_intel-v11.0_ofed/lib/libmpich.a(ibv_channel_manager.o):(.bss+0x18): multiple definition of  
`debug'
/scratch/cneale/exe/intel/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a(gmx_fatal.o):(.bss+0x530): first defined  
here

make[3]: *** [grompp] Error 1
make[3]: Leaving directory  
`/scratch/cneale/exe/intel/gromacs-4.0.5/src/kernel'

make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/scratch/cneale/exe/intel/gromacs-4.0.5/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/scratch/cneale/exe/intel/gromacs-4.0.5/src'
make: *** [all-recursive] Error 1


could this 'debug' be the one int calls like this? I at first looked  
for a debug() function but didn't find any.


$ grep debug src/gmxlib/*.c
...
main.c:  if (debug) {
main.c:fprintf(debug,"This is simulation %d",cr->ms->sim);
main.c:  fprintf(debug,", local number of nodes %d, local nodeid %d",
main.c:fprintf(debug,"\n\n");
...

Thanks,
Chris

#3

-- original message --

Hello all,

I have built MVAPICH2-1.4rc1 with Infiniband support on a CentOS 5.3 box and
am trying to build gromacs-4.0.5 with MPI support.

make is failing with the following error message:

mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -std=gnu99 -o grompp grompp.o
./.libs/libgmxpreprocess_mpi.a -L/usr/lib64 ../mdlib/.libs/libmd_mpi.a
/<...snip..>/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a
../gmxlib/.libs/libgmx_mpi.a -lxml2 -lnsl -lfftw3f -lm -lX11

/usr/local/lib/libmpich.a(ibv_channel_manager.o):(.bss+0x10): multiple
definition of `debug'
<..snip..>/gromacs-4.0.5/src/gmxlib/.libs/libgmx_mpi.a(gmx_fatal.o):(.bss+0x0):
first defined here
collect2: ld returned 1 exit status
make[3]: *** [grompp] Error 1

It looks like 'debug' is conflicting in both MVAPICH2 and in Gromacs.

Any suggestions?

Thanks,

Jerry.
Research Systems Administrator
SBGrid


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Re: [gmx-users] error in ffG43a1p force field

[Justin A. Lemkul]

Thamu wrote:

Hi,

i am trying to run md for protein-peptide complex. the peptide has
phosphorylated tyrosine.

i got the following error when i run pdb2gmx

Fatal error:
Error in hdb file ffG43a1p.hdb:
Wrong number of control atoms (2 iso 3) on line:


So, did you follow Mark's advice and read section 5.6.2?  Repeating a question 
without reference to previous help is usually a fast way to get ignored. 
Demonstrate that you are willing to help yourself before you expect to get more 
free help :)


This is indeed a formatting issue.  The ffG43a1p force field was designed for 
use with Gromacs-3.1.x, when formatting of these files was slightly different. 
They are quite easy to fix, if you read the manual.


-Justin


   11N-CCA

I also tried with phosphoserine, i got the same error as for 
phosphotyrosine.

I am using gromacs-4.0.2.


I would greatly appreciate if some one help me to solve this error.

Thanking you,

Yours sincerely,
Thamu




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] appropriate values fot tau_t and tau_p

[Berk Hess]

Hi,

You do not mention your the values you tried, nor other critical mdp parameters,
nor the property you are looking for, so it is difficult to help you.

In general, the larger you make tau_t and tau_p, the better things should get.
tau_p should be larger than tau_t, otherwise you might induce oscillations
by couplings between the thermo and barostat.

Berk

> From: rolf.is...@rwth-aachen.de
> To: gmx-users@gromacs.org
> Date: Fri, 24 Jul 2009 10:51:16 +0200
> Subject: [gmx-users] appropriate values fot tau_t and tau_p
> 
> Dear all,
> 
> I'm trying to receive thermal properties of a LJ liquid by performing a NPT 
> simulation. To ensure the simulation is in the canonic ensemble, I've chosen 
> the Nose-Hoover thermostat and the Parrinello-Rahmann barostat. I performed 
> several runs with different values for tau_t and tau_p. The results showed, 
> that the property which I am looking for depends on the value of these two 
> parameters. Does anybody know, how to chose these values to get fluctuations, 
> which correspond to the canonical ensemble?
> 
> Rolf
> 
> 
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[gmx-users] appropriate values fot tau_t and tau_p

[Rolf Erwin Isele-Holder]

Dear all,

I'm trying to receive thermal properties of a LJ liquid by performing a NPT 
simulation. To ensure the simulation is in the canonic ensemble, I've chosen 
the Nose-Hoover thermostat and the Parrinello-Rahmann barostat. I performed 
several runs with different values for tau_t and tau_p. The results showed, 
that the property which I am looking for depends on the value of these two 
parameters. Does anybody know, how to chose these values to get fluctuations, 
which correspond to the canonical ensemble?

Rolf


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[gmx-users] error in ffG43a1p force field

[Thamu]

Hi,

i am trying to run md for protein-peptide complex. the peptide has
phosphorylated tyrosine.

i got the following error when i run pdb2gmx

Fatal error:
Error in hdb file ffG43a1p.hdb:
Wrong number of control atoms (2 iso 3) on line:
   11N-CCA

I also tried with phosphoserine, i got the same error as for
phosphotyrosine.
I am using gromacs-4.0.2.


I would greatly appreciate if some one help me to solve this error.

Thanking you,

Yours sincerely,
Thamu
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