Re: [gmx-users] Re:On the usage of g_sas

[Justin Lemkul]

On 10/8/13 10:39 PM, Jernej Zidar wrote:

Dear Justin,
   Thanks for the help.

   That's what the manual says about the "-f_index" switch:
"Determine from a group in the index file what are the hydrophobic
atoms rather than from the charge"



Ah, I see now.  I misread the initial post.  The help paragraph in g_sas made no 
mention of this feature, but it is indeed listed.



What confuses me is that this is the only thing related to the matter,
no word about the naming conventions. Even ol' fella Google can't find
anything related to this issue.



Naming conventions?

I've never heard of anyone needing to use this feature, as the definition of 
hydrophobicity is generally quite robust.  I would suggest trying the default 
behavior first to determine if the result is suitable, unless you've already 
done this, in which case it would be useful to discuss if you have any 
reservations about the output you obtained.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
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[gmx-users] Re:On the usage of g_sas

[Jernej Zidar]

Dear Justin,
  Thanks for the help.

  That's what the manual says about the "-f_index" switch:
"Determine from a group in the index file what are the hydrophobic
atoms rather than from the charge"

What confuses me is that this is the only thing related to the matter,
no word about the naming conventions. Even ol' fella Google can't find
anything related to this issue.

Best,
Jernej

> On 10/8/13 7:27 AM, Jernej Zidar wrote:
>> Hi,
>>I would like to use g_sas to determine the surface properties of an
>> organic molecule and was wondering whether to trust g_sas in picking the
>> hydrophobic/hydrophilic atoms. I also saw one can supply an option index
>> file -f_index) for that but nothing is said about the form of this file.
>> Which option is better? I'm using the Charmm-generalized forcefield.
>>
>
> The index file taken by g_sas serves the function of any other Gromacs 
> program;
> it allows you to choose special calculation and/or output groups.  It doesn't
> let you choose which atoms are hydrophobic or hydrophilic, AFAIK.  The choice 
> is
> made based on the charges read in the .tpr file.  If |q| < 0.2, the atom is
> hydrophobic, otherwise it is hydrophilic.  If that choice doesn't suit you, 
> you
> can either modify the code or create a fake topology (for the purpose of
> analysis only!) with different charges that lead to different assignments.
>
> -Justin
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[gmx-users] CHARMM36 force field available for GROMACS

[Justin Lemkul]

All,

I am pleased to announce the immediate availability of the latest CHARMM36 force 
field in GROMACS format.  You can obtain the archive from our lab's website at 
http://mackerell.umaryland.edu/CHARMM_ff_params.html.


The present version contains up-to-date parameters for proteins, nucleic acids, 
lipids, some carbohydrates, CGenFF version 2b7, and a variety of of other small 
molecules.  Please refer to forcefield.doc, which contains a list of citations 
that describe the parameters, as well as the CHARMM force field files that were 
used to generate the distribution.


We have validated the parameters by comparing energies of a wide variety of 
molecules within CHARMM and GROMACS and have found excellent agreement between 
the two.  If anyone has any issues or questions, please feel free to post them 
to this list or directly to me at the email address below.


Happy simulating!

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Is Gromos force field 45a3 out of dated?

[Tsjerk Wassenaar]

Hi Lin,

I would say that it is not correct to call 45a3 deprecated. Like other
force fields, GROMOS 45a3 is also the result of careful parameterization.
The later GROMOS forcefields 53a5, 53a6, 54a7 and 54a8, took of a
completely different approach in parameterization, and are in that respect
not so much superseding, but rather complementary. Personally, I have been
and am still suspicious regarding these newer force fields, possibly with
the exception of 54a8. In 2006 I performed a statistical comparison of
simulations performed with 43a2 (overall similar to 45a3), and we found
that there were differences that could be related to the number of charged
residues. These residues were not reparameterized between 45a3 and 53a6,
which means that 53a6 (and 54a7) actually consists of a part which was
reparameterized and a part which was not, or at least not against the free
enthalpy of solvation. The consequence of this was that the new force field
was not consistent and could give rise to larger RMSD values and larger
radii of gyration, with the extent correlating with the number of charged
residues. This can be turned around: 45a3 is likely to give more stable
structures than the newer force fields and it is improbable that 45a3 would
give partial unfolding as artifact.

For the newest version, 54a8, the charged residues have also been
reparameterized and the result set should be consistent again.

I hope this is of some use to you.

Cheers,

Tsjerk


On Tue, Oct 8, 2013 at 7:30 PM, Chih-Ying Lin wrote:

> Hello,
> I submitted a paper and get rejected immediately by editor because of the
> following comment.
>
> "The simulations described here rely on an outdated force field (Gromos
> 45a3) and I suspect that the partial unfolding described here is at least
> in part due to force field artifacts. "
>
>
> Our simulation work fit the results from the experimental work quite well
> but the editor returned his suspicion.
>
>
> Is the force field Gromos 45a3 outdated?
> Could anyone refer me more details about the force field of Gromos 45a3?
> Could anyone refer me about any cases of the broken simulation from the
> force field artifacts?
>
>
> Thank you
> Lin
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[gmx-users] Iron(III) Chloride in water

[Jonathan Saboury]

I want to simulate Iron(III) Chloride in water (in order to test some iron
sequestering agents).

I've tried to use acpype to generate an iron ion but it errors.

So I used genion and labelled the positive ion "FE" with charge of 3.
However grompp does not recognize the atom "FE".

My question is how would I simulate this?

Commands: http://pastebin.com/raw.php?i=0B3EW7mF
Files: http://www.sendspace.com/file/rc8el9

Thank you!
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[gmx-users] Is Gromos force field 45a3 out of dated?

[Chih-Ying Lin]

Hello,
I submitted a paper and get rejected immediately by editor because of the
following comment.

"The simulations described here rely on an outdated force field (Gromos
45a3) and I suspect that the partial unfolding described here is at least
in part due to force field artifacts. "


Our simulation work fit the results from the experimental work quite well
but the editor returned his suspicion.


Is the force field Gromos 45a3 outdated?
Could anyone refer me more details about the force field of Gromos 45a3?
Could anyone refer me about any cases of the broken simulation from the
force field artifacts?


Thank you
Lin
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[gmx-users] Re: questions

[Tsjerk Wassenaar]

Dear Dwey,

Please direct questions like this to the gromacs user list, after asserting
that the answer has not already been given. In addition, please read
http://md.chem.rug.nl/~mdcourse/molmod2012/md.html

Regards,

Tsjerk


On Tue, Oct 8, 2013 at 5:35 PM, Dwey  wrote:

> Dear Tsjerk,
>
>I saw a discussion related to "solute at the center" on gmx-users.
> (See
> http://lists.gromacs.org/pipermail/gmx-users/2011-October/065292.html)
>
> I have similar issues of centering a protein in water.  After I add
> water into a box of dodecahedron, water did not cover the whole
> protein and protein is NOT placed in the center of water, although
> protein indeed is located in the center of box.
>
> like
> editconf_mpi -c -f protein.gro -o protein_box.gro -bt dodecahedron -d 1.2
>
> ( Note that increasing a box size is not an good option because it
> will take more much time in MD production)
>
> See the resulted image attached
>
> Base on previous discussion, I wonder if you can help me center the
> protein in the water.  ( I already tried commands many times like
> trjconv and editconf but in vain)
>
> Please kindly advise.
>
> Many thanks.
> Dwey
>



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Re: [gmx-users] Question about installing DSSP on Ubuntu 12.10

[Justin Lemkul]

On 10/8/13 7:28 AM, Mass wrote:

  I am trying to install "DSSP" in Ubuntu 12.10, I just download it from Ubuntu 
software centre but when I run it I am getting the following error, any solution? I have 
checked all the mail list archive and could not solve my problem
Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddZGP3ET ddjex0J9 > /dev/null 
2> /dev/null



You probably need to set -ver appropriately in your do_dssp command.


I google it and found this on ubuntu forum but I followed it and still I am 
getting error
up vote
0
down vote
accept DSSP is not in official ubuntu repositories, but you can install it 
manually:
sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O 
/usr/local/bin/dssp
or
sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O 
/usr/local/bin/dssp
And for the end:
sudo chmod a+x /usr/local/bin/dssp

   I have done this but still I am getting Fatal error: DSSP executable 
(/opt/dssp/bin/dssp) does not exist (use setenv DSSP) –


If you have set the $DSSP environment variable to point to /opt/dssp/bin/dssp, 
then you should get a fatal error, because based on the above commands, your 
dssp is in /usr/local/bin/dssp, which is the default location where do_dssp 
looks for it.  If $DSSP is set, it overrides the default, which in your case is 
causing problems.



  Also appreciate if any one can give simple and step-by step instruction to 
insall dssp-2.2.1 from website. I mean after downloading dssp-2.2.1.tgz and 
extracting it what should I do? –



Unzip the archive, compile from source if you are downloading source (ignore if 
you are downloading a binary), move the binary wherever you want it, set $DSSP 
only if you are not putting it in /usr/local/bin.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] On the usage of g_sas

[Justin Lemkul]

On 10/8/13 7:27 AM, Jernej Zidar wrote:

Hi,
   I would like to use g_sas to determine the surface properties of an
organic molecule and was wondering whether to trust g_sas in picking the
hydrophobic/hydrophilic atoms. I also saw one can supply an option index
file -f_index) for that but nothing is said about the form of this file.
Which option is better? I'm using the Charmm-generalized forcefield.



The index file taken by g_sas serves the function of any other Gromacs program; 
it allows you to choose special calculation and/or output groups.  It doesn't 
let you choose which atoms are hydrophobic or hydrophilic, AFAIK.  The choice is 
made based on the charges read in the .tpr file.  If |q| < 0.2, the atom is 
hydrophobic, otherwise it is hydrophilic.  If that choice doesn't suit you, you 
can either modify the code or create a fake topology (for the purpose of 
analysis only!) with different charges that lead to different assignments.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Can I generate Pulf files after mD running?

[Justin Lemkul]

On 10/7/13 9:41 PM, Yoochan,Myung wrote:

Dear gmx-users,

I have just finished umbrella MD but I missed to type pullf/pullx options
on mdrun.



If you omitted the pull-nstfout and/or pull-nstxout options in the .mdp file, 
their default values are taken and the files should have been produced.  If you 
did not specify file names on the mdrun command line, indeed there are some 
naming clashes that mangle the output.



So, can I get pullf/pullx .xvg files from mdrun results?



Possibly from a correct input file and mdrun -rerun, but I don't know if pulling 
options will work in -rerun mode.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Question about installing DSSP on Ubuntu 12.10

[Mass]

 I am trying to install "DSSP" in Ubuntu 12.10, I just download it from Ubuntu 
software centre but when I run it I am getting the following error, any 
solution? I have checked all the mail list archive and could not solve my 
problem
Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddZGP3ET ddjex0J9 > 
/dev/null 2> /dev/null
 
I google it and found this on ubuntu forum but I followed it and still I am 
getting error 
up vote
0
down vote
accept DSSP is not in official ubuntu repositories, but you can install it 
manually:
sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O 
/usr/local/bin/dssp 
or
sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O 
/usr/local/bin/dssp 
And for the end:
sudo chmod a+x /usr/local/bin/dssp 
 
  I have done this but still I am getting Fatal error: DSSP executable 
(/opt/dssp/bin/dssp) does not exist (use setenv DSSP) –  
 Also appreciate if any one can give simple and step-by step instruction to 
insall dssp-2.2.1 from website. I mean after downloading dssp-2.2.1.tgz and 
extracting it what should I do? – 

Thanks
Mehil Massteird
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[gmx-users] On the usage of g_sas

[Jernej Zidar]

Hi,
  I would like to use g_sas to determine the surface properties of an
organic molecule and was wondering whether to trust g_sas in picking the
hydrophobic/hydrophilic atoms. I also saw one can supply an option index
file -f_index) for that but nothing is said about the form of this file.
Which option is better? I'm using the Charmm-generalized forcefield.

Thanks in advance for the advice,
Jernej Zidar


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Windows: Re-Boot, Linux: Be-Root.
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RE: [gmx-users] Regarding lipid bilayer

[Kukol, Andreas]

And apparently you have only 6438 atoms in system_inflated.gro. So that is the 
source of the error.

>-Original Message-
>From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
>boun...@gromacs.org] On Behalf Of hasthi
>Sent: 08 October 2013 05:56
>To: gmx-users@gromacs.org
>Subject: [gmx-users] Regarding lipid bilayer
>
>Dear All,
>   I am trying to follow lipid bilayer simulation tutorial,I am 
> getting struck at
>energy minimization same step after generating system_inflated.gro file. I get
>the same error,
>
>Fatal error:
>Invalid line in system_inflated.gro for atom 6439:
>  25.67360  25.77400   6.59650
>I checked my system_inflated.gro and system.gro files too, the number of
>atoms in the second line are 6538 and 17503 respectively.
>
>I cannot figure out this error. Please help me in fixing this issue.
>
>Regards,
>V.Hasthi
>Student
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Re: [gmx-users] Re: g_hydorder

[Nidhi Katyal]

First I created index file with all oxygen atoms of water molecules using
make_ndx -f lys_full.gro -o index_soloxy.ndx
Then I used g_hydorder -f lys_full.xtc -s lys_full.tpr -n index_soloxy.ndx
-or file1.out file2.out

Following output appeared:
Program g_hydorder, VERSION 4.6.3
Source code file: /root/gromacs-4.6.3/src/tools/gmx_hydorder.c, line: 702

Fatal error:
No or not correct number (2) of output-files: 1
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Please guide me in filing redmine issue. I have read following link:
http://www.gromacs.org/Developer_Zone/Redmine

But could not locate link to file redine issue.


On Wed, Oct 2, 2013 at 12:41 AM, David van der Spoel
wrote:

> On 2013-10-01 19:51, Nidhi Katyal wrote:
>
>> Please provide me with necessary guidance. I have already posted this
>> thrice but have not got a single reply
>> Thanks in advance.
>>
>>
>> On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal *
>> *wrote:
>>
>>  Hello everyone,
>>>
>>> I would like to calculate angle tetrahedral order parameter of water
>>> molecules as defined by  Chau et al (eq 3). I am using g_hydorder of
>>> gromacs 4.6.3 with my index group containing all oxygen atoms of water:
>>> g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out
>>> file_2.out -n index.ndx
>>> I am getting following error;
>>> No or not correct number (2) of output files :1
>>>
>>
> Please give exact command line with file names and output cut-and pasted.
> The program needs indeed two output files of both types.
>
> It seems that your command line is ok nevertheless.
>
> Please file a redmine issue and assign it to me.
>
>
>  It seems from above that correct number should be 2 but user is supplying
>>> only 1 and so is the error. But I am giving names of two output files.
>>> Also, I am unable to understand what exactly is contained in these
>>> two/four output files. I tried to comprehend this by looking at
>>> gmx_hydorder.c and could make a guess that I actually need sgmol/sgmean
>>> (variables as defined in program) as the final output.
>>> Please help me understand the usage of this command in order to fulfill
>>> my
>>> aim.I have posted this twice but have not got a single reply.
>>> Thanks in advance.
>>>
>>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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