[gmx-users] Re: gmx-users Digest, Vol 85, Issue 114

marco miele marco.miele75 at gmail.com
Tue May 17 12:00:09 CEST 2011 

2011/5/17  <gmx-users-request at gromacs.org>:
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> Today's Topics:
>
>   1. RE: "Command Not Found" (Natalie Stephenson)
>   2. g_energy (Thomas Koller)
>   3. QMMM+NMA (Yao Yao)
>   4. compilation of g_hbond after bugfix (bipin singh)
>   5. Re: compilation of g_hbond after bugfix (Mark Abraham)
>   6. about side chain and structure rifinement (marco miele)
>   7. Re: about side chain and structure rifinement (Thomas Evangelidis)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 16 May 2011 15:19:54 +0000
> From: Natalie Stephenson
>        <Natalie.Stephenson at postgrad.manchester.ac.uk>
> Subject: RE: [gmx-users] "Command Not Found"
> To: "jalemkul at vt.edu" <jalemkul at vt.edu>, Discussion list for GROMACS
>        users   <gmx-users at gromacs.org>
> Message-ID:
>        <037BC2AE05ACF5459BEC1ACBFC4D9142036FD6 at MBXP06.ds.man.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Thanks loads ... that worked perfectly!! Environment configured!! :D
> xxx
>
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at 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-bounces at gromacs.org
>> [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul
>> [jalemkul at 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
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>
> --
> ========================================
>
> 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
>
> ========================================
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>
> ------------------------------
>
> Message: 2
> Date: Mon, 16 May 2011 23:37:45 +0200
> From: "Thomas Koller" <koller-thomas at gmx.de>
> Subject: [gmx-users] g_energy
> To: <gmx-users at gromacs.org>
> Message-ID: <471F6DDB671D4EE78F1A3F5E42ED221F at ThomasPC>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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
> -------------- next part --------------
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> ------------------------------
>
> Message: 3
> Date: Mon, 16 May 2011 17:17:40 -0700 (PDT)
> From: Yao Yao <yao0o at ymail.com>
> Subject: [gmx-users] QMMM+NMA
> To: gmx-users at gromacs.org
> Message-ID: <292062.73420.qm at web120419.mail.ne1.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
>
> 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
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 17 May 2011 11:10:11 +0530
> From: bipin singh <bipinelmat at gmail.com>
> Subject: [gmx-users] compilation of g_hbond after bugfix
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: "er..."@xray.bmc.uu.se
> Message-ID: <BANLkTin8GTv7V1g76d4xso15kKfsD4A4=g at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 17 May 2011 15:54:10 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] compilation of g_hbond after bugfix
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4DD20D82.5030007 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 17 May 2011 11:05:15 +0200
> From: marco miele <marco.miele75 at gmail.com>
> Subject: [gmx-users] about side chain and structure rifinement
> To: gmx-users at gromacs.org
> Message-ID: <BANLkTimJT4Jh+EAKL=jKXRpjRc_JuBmFYg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi everyone
> My question is that I have a receptor protein modeled which have some
> problem with side chain angles, I would like to know if is good to
> apply OPLS ff in vacuum to improve the side chain in particularly and
> structure in general.
> what you suggest me.
> Cheer marco
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 17 May 2011 12:20:19 +0300
> From: Thomas Evangelidis <tevang3 at gmail.com>
> Subject: Re: [gmx-users] about side chain and structure rifinement
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BANLkTikhcJ_EnVjHKLzffnk5DRKedVBguQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> A MM ff like OPLS will probably do your job. However CASP experiments show
> that knowledge-based potentials like the one Rosetta implements, produce
> more physically realistic results. If you only want to improve the
> side-chain conformations, I'd suggest to use a program that employs rotamer
> libraries like SCWRL4.

Thank you very much to answer me quickly.
I have already utilized SCRWRL4,
It have improve some side chain but other not.
So I thought to improve trough to MD OPLS the rest of structure and
side chain, too.
I now try in this way and then I'll send you the results if you're
interested on it.
cheer
marco


>
>
> On 17 May 2011 12:05, marco miele <marco.miele75 at gmail.com> wrote:
>
>> Hi everyone
>> My question is that I have a receptor protein modeled which have some
>> problem with side chain angles, I would like to know if is good to
>> apply OPLS ff in vacuum to improve the side chain in particularly and
>> structure in general.
>> what you suggest me.
>> Cheer marco
>> --
>> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
>
> Biomedical Research Foundation, Academy of Athens
>
> 4 Soranou Ephessiou , 115 27 Athens, Greece
>
> email: tevang at bioacademy.gr
>
>          tevang3 at gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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> End of gmx-users Digest, Vol 85, Issue 114
> ******************************************
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