[gmx-users] do_dssp file format
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Thu Jan 10 20:41:23 CET 2008
I used the following command
./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part is show below. I obtained a segmentation fault.
Maybe it is not a the good command. Remember that my trajectories are not made/compatible with GROMACS and i have only a pdb coordinates of my MD.
Any help will be appreciate
Stefane
ATOM 1 CAY ACE 1 6.421 -7.877 -11.574 -0.27 0.00
ATOM 2 HA1 ACE 1 6.050 -8.804 -12.062 0.09 0.00
ATOM 3 HA2 ACE 1 6.728 -7.203 -12.402 0.09 0.00
ATOM 4 HA3 ACE 1 5.529 -7.417 -11.098 0.09 0.00
ATOM 5 C ACE 1 7.470 -8.140 -10.510 0.51 0.00
ATOM 6 O ACE 1 7.594 -9.280 -10.074 -0.51 0.00
ATOM 7 N GLY 2 8.125 -7.096 -10.030 -0.47 0.00
ATOM 8 HN GLY 2 7.927 -6.156 -10.295 0.31 0.00
ATOM 9 CA GLY 2 8.970 -7.131 -8.819 -0.02 0.00
ATOM 10 HA1 GLY 2 8.889 -8.007 -8.193 0.09 0.00
ATOM 11 HA2 GLY 2 8.638 -6.265 -8.265 0.09 0.00
ATOM 12 C GLY 2 10.408 -6.734 -9.033 0.51 0.00
ATOM 13 O GLY 2 11.313 -7.365 -8.492 -0.51 0.00
ATOM 14 N ASP 3 10.647 -5.532 -9.599 -0.47 0.00
ATOM 15 HN ASP 3 9.863 -5.073 -10.011 0.31 0.00
ATOM 16 CA ASP 3 11.864 -4.806 -9.831 0.07 0.00
ATOM 17 HA ASP 3 12.713 -5.321 -9.406 0.09 0.00
ATOM 18 CB ASP 3 12.026 -4.347 -11.282 -0.28 0.00
ATOM 19 HB1 ASP 3 11.065 -4.008 -11.725 0.09 0.00
ATOM 20 HB2 ASP 3 12.877 -3.652 -11.448 0.09 0.00
ATOM 21 CG ASP 3 12.414 -5.579 -12.163 0.62 0.00
ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00
ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00
------------------------------
Message: 3
Date: Thu, 10 Jan 2008 13:03:30 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] do_dssp file format
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <1199988210.47865df210e6b at webmail.vt.edu>
Content-Type: text/plain; charset=ISO-8859-1
Quoting ABEL Stephane 175950 <Stephane.ABEL at cea.fr>:
> > Hi gromacs users
> >
> > For my work I have performed some simulations of a protein in water with an
> other MD software not compatible with >GROMACS. And I would like to compute
> the time evolution of the secondary structure of my protein, I know that the
> >with >the xpm2ps tool give in gromacs. Is it possible to have an (small)
> exemple of an .xpm file generated by the do_dssp >tools
>
> Just run a 10-step MD simulation and generate one yourself. Or convert
> your other trajectories into .pdb format and use that as input to
> do_dssp. You do not necessarily need a .tpr file for do_dssp, see "man
> do_dssp" under the "-s" flag.
>
> Mark
>
> Thanks Mark for your suggestions but it is not working for me So i have
> tested an other approach with VMD to obtain the secondary structure time
> series for my protein. The ouput graph obtained is not pretty, so i would
> like to make for a paper a same graph that i found in some gromacs papers.
> For this i need to convert the output datas file of VMD to gromacs xpm file
> obtained with do_dssp with a script and convert it to ps with the xpm2ps
> tool. In gromacs documentation i can not find an exemple of xpm file
> generated with do_dssp. So it is possible to obtain from the gromacs users a
> small exemple of this file to see how the datas are arranged
What exactly is "not working?" As in, what commands are you issuing? Did the
MD fail, or the analysis of the trajectory? If you provide this type of
information, we may be able to help you better.
-Justin
>
> Thank you very much
>
> Stefane
> _______________________________________________
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>
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
------------------------------
Message: 4
Date: Thu, 10 Jan 2008 19:27:38 +0100
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Dihedral with parameters set to zero
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4786639A.6060806 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
van Bemmelen wrote:
> OK. Now I'm confused. What did you mean by the second part?
>
> Of course, when doing FEP with the B state different, you would
> gradually introduce a dihedral as lambda increases. But that would still
> mean that setting all dihedral parameters to 0 for the A state would be
> exactly equivalent to having no dihedral at all, only for the simulation
> at lambda=0.0. Right?
>
> Or did you mean something else?
>
> Thanks,
> Jeroen
>
> P.S. Actually, in such a setup one would probably run into trouble
> anyway because according to the manual the multipliciy cannot be
> perturbed. But let's ignore that for now.
but that can be solved by defining two dihedrals with different mult and
turn off one and turn on the other.
>
>
>> Date: Wed, 09 Jan 2008 20:41:19 +0100
>> From: David van der Spoel <spoel at xray.bmc.uu.se>
>> Subject: Re: [gmx-users] Dihedral with parameters set to zero
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4785235F.2090703 at xray.bmc.uu.se>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> van Bemmelen wrote:
>>> Hi guys,
>>>
>>> Probably too simple for you guys, but I just need to be sure:
>>>
>>> Am I right if I say that a GROMOS96 proper dihedral with all
>> parameters
>>> set to 0 (done automatically by grompp) is exactly equivalent to no
>>> proper dihedral at all, both with respect to all the energy terms and
>>> with respect to the dynamics? Or is there some catch I
>> haven't thought
>>> of?
>> that's correct, unless you would be doing FEP with the B state
>> different.
>>> Thanks,
>>> Jeroen
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se <http://folding.bmc.uu.se/>
------------------------------
Message: 5
Date: Thu, 10 Jan 2008 13:34:14 -0500
From: Chris Neale <chris.neale at utoronto.ca>
Subject: [gmx-users] Generating topology file for a molecule (FNP) not
in the gromacs library.
To: gmx-users at gromacs.org
Message-ID: <47866526.5030604 at utoronto.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
When actually building the topology I find it easiest to create the residues in the relevant .rtp and allow pdb2gmx to build the topology for you. However, all this does is correctly connect everything and put your parameters where they should be. All previous comments (in this thread and the hundreds of other threads on this topic) still apply about how to come up with the parameters... read the original papers and reproduce their methodology.
Chris.
>Dear users,
> I am working with PTP1B protein. Recently I
>tried to run it in gromacs along with an inhibitor
>{[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN-
>2-YL]-DIFLUORO-METHYL}-PHOSPHONIC ACID [FNP in short]. The
>problem is that gromacs does not recognize FNP and hence I
>am not able to generate a topology file of it using pdb2gmx. I
>tried using the The Dundee PRODRG server to generate the
>topology file with the pdb file as the input. The problem is
>that it does generate the topology file but without any
>hydrogens. Even the polar hydrogens information is not
>available inspite of it being a part of my input pdb file.
>Thus I am not able to use FNP with the polar hydrogens for my runs.
>
>If anyone has faced similar problems please do help if you can.
>
>Thanking you,
>Cheers.
------------------------------
Message: 6
Date: Thu, 10 Jan 2008 19:44:23 +0100 (CET)
From: "Prasad Gajula" <prasad.gajula at uni-osnabrueck.de>
Subject: [gmx-users] rmsd with average structure
To: gmx-users at gromacs.org
Message-ID:
<1622.131.173.9.199.1199990663.squirrel at webmail.rz.uni-osnabrueck.de>
Content-Type: text/plain;charset=iso-8859-1
Dear Groamcs users,
I calcualted the average structure from the simulation trajectory. when I
calculate the rmsd of the protein to this average sturture, it is giving
average rmsd of 0.16 nm. But, it is not clear for me why the average
sturcture is never adapted rmsd near (or equal) to zero. I did not
calculate the rmsd with respect to the starting structure either.
Any clue?
Thanks in advance!
------------------------------
Message: 7
Date: Thu, 10 Jan 2008 19:49:41 +0100
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] rmsd with average structure
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <478668C5.4030306 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Prasad Gajula wrote:
> Dear Groamcs users,
>
> I calcualted the average structure from the simulation trajectory. when I
> calculate the rmsd of the protein to this average sturture, it is giving
> average rmsd of 0.16 nm. But, it is not clear for me why the average
> sturcture is never adapted rmsd near (or equal) to zero. I did not
> calculate the rmsd with respect to the starting structure either.
> Any clue?
the average structure is unphysical, it may have long bonds etc.
> Thanks in advance!
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se <http://folding.bmc.uu.se/>
------------------------------
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