[gmx-users] inserting new residue
sadhna
sadhana at che.iitb.ac.in
Fri Jan 24 05:55:36 CET 2003
hi,
I mean that for other carbonyl bonds it shows two lines for double
bonds but for my residue it shows one line and when i go to the add
hydrogen menu the hydrogen gets added to the corbonyl oxygen also which it
should not!! It doesn't add hydrogen to the carbonyl oxygen for other
residues.
rgds
sadhna
> Message: 2
> Date: Thu, 23 Jan 2003 11:19:54 -0500 (GMT)
> From: sadhna <sadhana at che.iitb.ac.in>
> To: <gmx-users at gromacs.org>
> X-Scanned: By Symantec Carrier Scan Server
> Subject: [gmx-users] inserting new residue
> Reply-To: gmx-users at gromacs.org
>
>
> hi,
> I have inserted a new residue in the residue toplogy file. Gromacs
> accepts it but the problem is when i see it in web lab viewer it shows
> single bond for carbonyl oxygen(of the peptide bond) instead of double
> bond .
>
> Where could i have gone wrong?
>
>
> rgds
>
> sadhna
>
> Research Scholar
> Dept of Chemical Engg
> Indian Institute of Technology,Powai
> Mumbai-400076
> India
>
>
> --__--__--
>
> Message: 3
> Date: Wed, 22 Jan 2003 21:55:25 -0800
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> Subject: Re: [gmx-users] inserting new residue
> From: Erik Lindahl <lindahl at stanford.edu>
> To: gmx-users at gromacs.org
> Reply-To: gmx-users at gromacs.org
>
>
> On Thursday, January 23, 2003, at 08:19 AM, sadhna wrote:
>
> >
> > hi,
> > I have inserted a new residue in the residue toplogy file. Gromacs
> > accepts it but the problem is when i see it in web lab viewer it shows
> > single bond for carbonyl oxygen(of the peptide bond) instead of double
> > bond .
> >
> > Where could i have gone wrong?
> >
> >
> I'm not sure what you mean by single vs. double bond in the viewer; a
> "double bond" in Gromacs (and other MD programs) is just a normal bond
> that
>
> 1) is slightly shorter
> 2) has a higher force constant
> 3) has a dihedral to keep the group planar (if necessary)
>
> So, normally it will just look like a normal bond in a viewer.
>
> Cheers,
>
> Erik
>
>
> --__--__--
>
> Message: 4
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> Subject: Re: [gmx-users] DSSP problem
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Date: 23 Jan 2003 11:11:38 +0100
> Reply-To: gmx-users at gromacs.org
>
> On Wed, 2003-01-22 at 19:57, MOLTENI at unisi.it wrote:
> > Hi all
> >
> > I have a problem with the "do_dssp" GROMACS module on one of my MD
> > trajectories: it is a 8 ns trajectory of a peptide in water and, when I
> > run do_dssp on it, the output displays only the first 4440 ps (and the
> > program says "last frame: time 4440"), while when I run g_rms on the
> > same trajectory file, the output displays the whole 8 ns trajectory. Can
> > it be a problem due to file size, since it seems similar to the one
> > described in one of the recent e-mails I read on the list (two different
> > programs behave differently on the same file...)?
> >
> > some details:
> >
> > * the size of my file is 975.284 Mb (so, at least it isn't a "2 Gb
> > problem"..)
> File size is not the problem. Can you run the dssp in parts?
> E.g. do_dssp -b 5000?
> Do you see anything strange in the RMSD at 4400? It could be that dssp
> crashes for some reason, and that the program halts for that reason.
>
>
> > * I run do_dssp this way:
> > do_dssp -f trajectoryfile -s ....md1.tpr -o ss.xpm -dt 30
> >
> > and, as "group" I select the whole "protein" (without the solvent)
> This is correct
> >
> > By the way, is it ok to use always the .tpr file of the first MD run (it
> > should be the one related to the initial structure of the trajectory, if
> > I understand well) in case of multiple runs, for this kind of analysis
> > programs?
> Yes, the tpr is only used for atom names here.
>
> For most analysis it is necessary that tpr and xtc match exactly
> (watchout when using grompp -shuffle). For some analysis it doesn't
> matter, as long as the part you are analyzing is compatible. There is no
> good error checking though.
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576, 75123 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> --__--__--
>
> Message: 5
> Date: Thu, 23 Jan 2003 09:24:29 +0100
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To: gmx-users at gromacs.org
> X-Scanned: By Symantec Carrier Scan Server
> Subject: Re: [gmx-users] DSSP problem
> Reply-To: gmx-users at gromacs.org
>
> MOLTENI at unisi.it wrote:
> > Hi all
> >
> > I have a problem with the "do_dssp" GROMACS module on one of my MD
> > trajectories: it is a 8 ns trajectory of a peptide in water and, when I
> > run do_dssp on it, the output displays only the first 4440 ps (and the
> > program says "last frame: time 4440"), while when I run g_rms on the
> [...]
> >
> > * I run do_dssp this way:
> > do_dssp -f trajectoryfile -s ....md1.tpr -o ss.xpm -dt 30
>
> This is likely your problem: the '-dt 30' option calculates the modulo
> of the time stamp of the frams. Unfortunately, there are unavoidable
> rounding errors, which increase with larger numbers. At some point,
> the modulo result will be larger than the tolerance value we use, and
> the appropriate time frames will not be selected for analysis...
>
> There are two possible workarounds:
> * re-set the times on the frames using trjconv -timestep
> then run do_dssp -dt 30
> * first create a 30ps interval trajectory using trjconv -skip
> and use that trajectory with do_dssp
>
>
> --
> Groetjes,
>
> Anton
> ________ ___________________________________________________________
> | | Anton Feenstra |
> | . | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |---- | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands |
> | |---- | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> | ' __ | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> | / \ |-----------------------------------------------------------|
> | ( ) | Dept. of Biophysical Chemistry - University of Groningen |
> | \__/ | Nijenborgh 4 - 9747 AG Groningen - The Netherlands |
> | __ | Tel +31 50 363 4327 - Fax +31 50 363 4800 |
> | / \ | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton |
> | ( ) |-----------------------------------------------------------|
> | \__/ | "If You See Me Getting High, Knock Me Down" |
> | | (Red Hot Chili Peppers) |
> |________|___________________________________________________________|
>
>
> --__--__--
>
> Message: 6
> Date: Thu, 23 Jan 2003 11:08:45 +0100
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To: gmx-users at gromacs.org
> X-Scanned: By Symantec Carrier Scan Server
> Subject: [gmx-users] LJ potential definitions?
> Reply-To: gmx-users at gromacs.org
>
> Hi All,
>
>
> I am trying to figure out some strange desagreement between LJ potential
> definitions.
>
> From the Gromacs manual (p50/51) I have:
>
> E(r) = 4? ( (?/r)^12 - (?/r)^6 )
>
> but from Cornell et al. (& Kollman), JACS 117 (1995), eq. 1, I have:
>
> E(r) = A/(r^12) - B/(r^6)
> where (from Table 13): A = ? ?^12 and B = 2? ?^6
> (they use R for r and R* for ?)
> Rewriting this, gives the following:
>
> E(r) = ? ( (?/r)^12 - 2 (?/r)^6 )
>
> So the question is, compared to the 'Gromacs' formula, where did the
> factor 4 in 4? go, and second, where does the factor 2 for the sixth
> power term come from?
>
>
> --
> Groetjes,
>
> Anton
> ________ ___________________________________________________________
> | | Anton Feenstra |
> | . | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |---- | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands |
> | |---- | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> | ' __ | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> | / \ |-----------------------------------------------------------|
> | ( ) | Dept. of Biophysical Chemistry - University of Groningen |
> | \__/ | Nijenborgh 4 - 9747 AG Groningen - The Netherlands |
> | __ | Tel +31 50 363 4327 - Fax +31 50 363 4800 |
> | / \ | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton |
> | ( ) |-----------------------------------------------------------|
> | \__/ | "If You See Me Getting High, Knock Me Down" |
> | | (Red Hot Chili Peppers) |
> |________|___________________________________________________________|
>
>
> --__--__--
>
> Message: 7
> Date: Thu, 23 Jan 2003 11:54:52 +0100
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To: gmx-users at gromacs.org
> X-Scanned: By Symantec Carrier Scan Server
> Subject: Re: [gmx-users] LJ potential definitions?
> Reply-To: gmx-users at gromacs.org
>
> Anton Feenstra wrote:
> > Hi All,
> >
> >
> > I am trying to figure out some strange desagreement between LJ potential
> > definitions.
>
> I'll answer that one ;-)
> First, my aplogies; the sigma and epsilon got lost in code tables...
>
> The confusion stems from the relation between R* and sigma. R* is the
> distance at potential *minimum*, and sigma at *zero* potential. The
> relation is R* = sigma . 2^(1/6), which makes both formulae identical.
>
>
> --
> Groetjes,
>
> Anton
> ________ ___________________________________________________________
> | | Anton Feenstra |
> | . | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |---- | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands |
> | |---- | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> | ' __ | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> | / \ |-----------------------------------------------------------|
> | ( ) | Dept. of Biophysical Chemistry - University of Groningen |
> | \__/ | Nijenborgh 4 - 9747 AG Groningen - The Netherlands |
> | __ | Tel +31 50 363 4327 - Fax +31 50 363 4800 |
> | / \ | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton |
> | ( ) |-----------------------------------------------------------|
> | \__/ | "If You See Me Getting High, Knock Me Down" |
> | | (Red Hot Chili Peppers) |
> |________|___________________________________________________________|
>
>
>
> --__--__--
>
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