[gmx-users] inserting new residue
David
spoel at xray.bmc.uu.se
Thu Jan 23 19:10:41 CET 2003
On Fri, 2003-01-24 at 05:55, sadhna wrote:
> 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.
>
the program (web lab viewer) is less intelligent than you think. The
bond is probably a fraction too short. Measure it after em and check
whether it is correct. If not go back to your topology...
> 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
> > X-Scanned: By Symantec Carrier Scan Server
> > 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
> > X-Scanned: By Symantec Carrier Scan Server
> > 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) |
> > |________|___________________________________________________________|
> >
> >
> >
> > --__--__--
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> >
> >
> > End of gmx-users Digest
> >
>
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--
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 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
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