[gmx-users] Re: gmx-users digest, Vol 1 #729 - 15 msgs
Sergio Manzetti
sergio.manzetti at bio.uio.no
Tue Apr 15 12:56:01 CEST 2003
The model was built on 22% sequence hgomology. The structure binds NADP to
reduce an unknown substrate. The goal is to get the best candidate for
docking experimtents.
Sergio
At 11:02 15.04.2003 +0200, you wrote:
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>Today's Topics:
>
> 1. Simulation (Sergio Manzetti)
> 2. Re: (no subject) (David van der Spoel)
> 3. Re: SSE vs 3DNow! (David van der Spoel)
> 4. Re: Simulation (Ghermes Chilov)
> 5. rescaling PBC for PDB output (Alan Wilter Sousa da Silva)
> 6. about g_hbond (Alan Wilter Sousa da Silva)
> 7. Re: about g_hbond (Alan Wilter Sousa da Silva)
> 8. G_Energy calculation ?'s (DaJustice1 at aol.com)
> 9. where are RB dihedral force constants! (nanyu101)
> 10. Re: G_Energy calculation ?'s (David)
> 11. Re: where are RB dihedral force constants! (David)
> 12. RB dihedral and its force constants! (nanyu101)
> 13. Re: rescaling PBC for PDB output (David van der Spoel)
> 14. RB dihedral again and dihedral constants (nanyu101)
> 15. Re: how to prove the charges in rtp file! (Anton Feenstra)
>
>--__--__--
>
>Message: 1
>Date: Mon, 14 Apr 2003 12:32:58 +0200
>To: gmx-users at gromacs.org
>From: Sergio Manzetti <sergio.manzetti at bio.uio.no>
>Subject: [gmx-users] Simulation
>Reply-To: gmx-users at gromacs.org
>
>Didn't get an answer, so I try again:
>
>
>Hi all, in the past I have had many experiences with MD and the negative
>effects on protein structures and models. In this regard, I keep certain
>residues freezed for a better simulation outcome, which highly reduces
>"negative divergence" from the start model. Believe me, but the start model
>(if its from protein modelling) can be the best structural candidate all
>the way to 20% homology and when this is simulated it all becomes worst.
>In this regard I am trying various approaches to keep the reisudes from
>fluctuating in an exaggerated manner. One thing I thought about was to do
>simulations at 100K for a loong time, rather than 300K for a shorter
>period. Basically I am looking for smoother transitions to energy minimums
>because I think that the possibility to get stuck in a misfolded candidate
>is much higher at high temperatures given the higher number of candidates
>explored. In other words, I am looking for the "descense to a good minimum"
>from the initial model, rather than exhaustive search for a energy minimum.
>Are there other ways I can do such an approach except lowering the
>temperature?
>Sergio
>
>
>--__--__--
>
>Message: 2
>Subject: Re: [gmx-users] (no subject)
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>To: gmx-users at gromacs.org
>Date: 14 Apr 2003 16:57:25 +0200
>Reply-To: gmx-users at gromacs.org
>
>On Mon, 2003-04-14 at 10:42, Zhili Zuo wrote:
> > hello all:
> > I want to generate the topology for the ligand. But my ligand is
> composed of eight residues, six of them are GLU, LEU, ASP, VAL, GLU and
> PHe, and two of them are non-peptide residues in the middle.
> > when I made top file in www.davapc1.bioch.dundee.ac.uk, the hydrogens
> in all the carboxyl were missing and the coordinate of hydrogen to the
> nitrogen in the last GLU is "nan".
> >
> > How can I generate the proper topology of my ligand?
>You have to create new residues in the force field of your choice. (.rtp
>and .hdb file)
>See manual.
>
>
> > Thank you!!
> > 2003-04-14
> >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
>--
>Groeten, David.
>________________________________________________________________________
>Dr. David van der Spoel, Dept. of Cell & Mol. 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
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>--__--__--
>
>Message: 3
>Subject: Re: [gmx-users] SSE vs 3DNow!
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>To: gmx-users at gromacs.org
>Date: 14 Apr 2003 16:58:02 +0200
>Reply-To: gmx-users at gromacs.org
>
>On Mon, 2003-04-14 at 11:39, Ghermes Chilov wrote:
> > Dear GMX-users,
> >
> > Has anyone clearly checked out the profit of SSE in
> > comparison with 3DNow!? There were some tenuous discussions on
> > the list sometime ago, probably some details become more definite?
> >
>On new Athlons you have both, and SSE is slightly faster. That's the
>default now.
> > Ghermes Chilov
> > Moscow State University
> >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
>--
>Groeten, David.
>________________________________________________________________________
>Dr. David van der Spoel, Dept. of Cell & Mol. 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
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>--__--__--
>
>Message: 4
>Date: Mon, 14 Apr 2003 15:23:47 +0400
>From: Ghermes Chilov <Ghermes at belozersky.msu.ru>
>Organization: Belozersky Institute of PhysicoChemical Biology
>To: Sergio Manzetti <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Simulation
>Reply-To: gmx-users at gromacs.org
>
>Hello Sergio,
>
>Could you tell in more detail how did you obtain the starting model
>and what is the goal of your studies/simulations? You know, the final
>answer always guides your investigation from the beginning to end.
>
>Ghermes Chilov
>Moscow State University
>
>
>
>--__--__--
>
>Message: 5
>Date: Mon, 14 Apr 2003 11:54:56 -0300 (BRT)
>From: Alan Wilter Sousa da Silva <alan at biof.ufrj.br>
>To: <gmx-users at gromacs.org>
>Subject: [gmx-users] rescaling PBC for PDB output
>Reply-To: gmx-users at gromacs.org
>
>
>Hi List!
>
>=09I have a simulation with a lot of water. I just wonder if I could
>use trjconv to generate a PDB output with box smaller than the original
>one (just covering protein for example) and with water within the box, but
>excluding the waters outside the new box.
>
>Many thanks in advance for any suggestion or help.
>
>Cheers,
>
>-----------------------
>Alan Wilter S. da Silva
>-----------------------
> Laborat=F3rio de F=EDsica Biol=F3gica
> Instituto de Biof=EDsica Carlos Chagas Filho
> Universidade do Brasil/UFRJ
> Rio de Janeiro, Brasil
>
>
>--__--__--
>
>Message: 6
>Date: Mon, 14 Apr 2003 13:26:41 -0300 (BRT)
>From: Alan Wilter Sousa da Silva <alan at biof.ufrj.br>
>To: <gmx-users at gromacs.org>
>Subject: [gmx-users] about g_hbond
>Reply-To: gmx-users at gromacs.org
>
>
>Hi List!
>
>=09I know that including '-ins' with g_hbond, solvent molecules will
>be evaluated.
>
>=09However, the unique result one gots is just the insert.dat file?
>
>Thanks in advance for any help.
>
>Cheers,
>
>-----------------------
>Alan Wilter S. da Silva
>-----------------------
> Laborat=F3rio de F=EDsica Biol=F3gica
> Instituto de Biof=EDsica Carlos Chagas Filho
> Universidade do Brasil/UFRJ
> Rio de Janeiro, Brasil
>
>
>--__--__--
>
>Message: 7
>Date: Mon, 14 Apr 2003 13:42:30 -0300 (BRT)
>From: Alan Wilter Sousa da Silva <alan at biof.ufrj.br>
>To: <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] about g_hbond
>Reply-To: gmx-users at gromacs.org
>
>To myself
>
>I found that hbmap.xpm plots the information about water molecules
>intermediating H-bonds. However, it leads me to another question: what is
>the difference between '(blue) Inserted' and '(pink) Present & Inserted'?
>
>I really would appreciate any help.
>
>Cheers,
>
>On Mon, 14 Apr 2003, Alan Wilter Sousa da Silva wrote:
>
> >
> > Hi List!
> >
> > =09I know that including '-ins' with g_hbond, solvent molecules will
> > be evaluated.
> >
> > =09However, the unique result one gots is just the insert.dat file?
> >
> > Thanks in advance for any help.
> >
> > Cheers,
> >
> > -----------------------
> > Alan Wilter S. da Silva
> > -----------------------
> > Laborat=F3rio de F=EDsica Biol=F3gica
> > Instituto de Biof=EDsica Carlos Chagas Filho
> > Universidade do Brasil/UFRJ
> > Rio de Janeiro, Brasil
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
>
>--=20
>-----------------------
>Alan Wilter S. da Silva
>-----------------------
> Laborat=F3rio de F=EDsica Biol=F3gica
> Instituto de Biof=EDsica Carlos Chagas Filho
> Universidade do Brasil/UFRJ
> Rio de Janeiro, Brasil
>
>
>--__--__--
>
>Message: 8
>From: DaJustice1 at aol.com
>Date: Mon, 14 Apr 2003 21:03:28 EDT
>To: gmx-users at gromacs.org
>Subject: [gmx-users] G_Energy calculation ?'s
>Reply-To: gmx-users at gromacs.org
>
>
>--part1_14c.1e351ea7.2bccb460_boundary
>Content-Type: text/plain; charset="US-ASCII"
>Content-Transfer-Encoding: 7bit
>
>Hello Everyone,
>
>I have a quick question. How do you calculate the potential energy from
>Coulomb interactions with a .edr file. I have used "Coulomb-14" and
>"Coulomb-SR". I have looked in the manual for descriptions of both, and
>have found very little about them. I know it is probably a simple question,
>but it would help me out a bunch.
>
>Thank you,
>David
>
>--part1_14c.1e351ea7.2bccb460_boundary
>Content-Type: text/html; charset="US-ASCII"
>Content-Transfer-Encoding: quoted-printable
>
>Hello Everyone,
>
>I have a quick question. How do you calculate the potential energy fr= om
>Coulomb interactions with a .edr file. I have used "Coulomb-14" an= d
>"Coulomb-SR". I have looked in the manual for descriptions of both,= and
>have found very little about them. I know it is probably a simpl= e
>question, but it would help me out a bunch.
>
>Thank you,
>David
>--part1_14c.1e351ea7.2bccb460_boundary--
>
>--__--__--
>
>Message: 9
>From: nanyu101 <nanyu101 at sina.com>
>To: gmx-users at gromacs.org
>Date: Tue, 15 Apr 2003 14:30:04 +0800
>Subject: [gmx-users] where are RB dihedral force constants!
>Reply-To: gmx-users at gromacs.org
>
>Dear gmx-users,
>
> If I want to simulate my system with RB dihedral type,how can I find
> the other force constants in ff*bond.itp file?I just found there is only
> one force constant in ff*bond.itp file,where is the others? Would you
> please tell me this?
>
>Best wishes,
>XIanhui Wu
>______________________________________
>
>===================================================================
>
>--__--__--
>
>Message: 10
>Subject: Re: [gmx-users] G_Energy calculation ?'s
>From: David <spoel at xray.bmc.uu.se>
>To: gmx-users at gromacs.org
>Date: 15 Apr 2003 07:49:46 +0200
>Reply-To: gmx-users at gromacs.org
>
>On Tue, 2003-04-15 at 03:03, DaJustice1 at aol.com wrote:
> > Hello Everyone,
> >
> > I have a quick question. How do you calculate the potential energy from
> > Coulomb interactions with a .edr file. I have used "Coulomb-14" and
> > "Coulomb-SR". I have looked in the manual for descriptions of both, and
> > have found very little about them. I know it is probably a simple
> question,
> > but it would help me out a bunch.
>If you just want Coulomb energy
>use Coul-14, Coulomb-SR and Coulomb-LR
>if you want Potential energy, use Potential
>if you have a multicomponent system and you have specified energy groups
>then you will find even more terms for the interaction energies further
>down.
>
>--
>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
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>--__--__--
>
>Message: 11
>Subject: Re: [gmx-users] where are RB dihedral force constants!
>From: David <spoel at xray.bmc.uu.se>
>To: gmx-users at gromacs.org
>Date: 15 Apr 2003 07:51:10 +0200
>Reply-To: gmx-users at gromacs.org
>
>On Tue, 2003-04-15 at 08:30, nanyu101 wrote:
> > Dear gmx-users,
> >
> > If I want to simulate my system with RB dihedral type,how can I find
> the other force constants in ff*bond.itp file?I just found there is only
> one force constant in ff*bond.itp file,where is the others? Would you
> please tell me this?
> >
>There is only one real Ryckaert Bellemans potential, for alkanes. If you
>want others you have to define them yourself. E.g. the OPLS force field
>has lots of them.
> > Best wishes,
> > XIanhui Wu
> > ______________________________________
> >
> > ===================================================================
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
>--
>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
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>--__--__--
>
>Message: 12
>From: nanyu101 <nanyu101 at sina.com>
>To: gmx-users at gromacs.org
>Date: Tue, 15 Apr 2003 11:08:22 +0800
>Subject: [gmx-users] RB dihedral and its force constants!
>Reply-To: gmx-users at gromacs.org
>
>Dear gmx-users,
>
> I want to use RB dihedral type for my simulation.But I can't find the
> force constants in ffG43a2bond.itp file.In this itp file, there is only
> one force constant,but RB dihedral type has five force constants.Where
> are they?
>
>Thanks very much.
>
>Best wishes,
>XIanhui Wu
>______________________________________
>
>===================================================================
>
>--__--__--
>
>Message: 13
>Subject: Re: [gmx-users] rescaling PBC for PDB output
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>To: gmx-users at gromacs.org
>Date: 15 Apr 2003 10:34:15 +0200
>Reply-To: gmx-users at gromacs.org
>
>On Mon, 2003-04-14 at 16:54, Alan Wilter Sousa da Silva wrote:
> >=20
> > Hi List!
> >=20
> > I have a simulation with a lot of water. I just wonder if I could
> > use trjconv to generate a PDB output with box smaller than the original
> > one (just covering protein for example) and with water within the box, bu=
>t
> > excluding the waters outside the new box.
>
>Your new box wouldn't be periodc anymore, so this is not entirely
>trivial (although it would be easy to code). Furthermore your protein
>may diffuse. What you can do is to
>order the trajectory (trjorder) to sort them according to distance to
>the protein. Drawback is that you will have different water molecules at
>each step.
>
> >=20
> > Many thanks in advance for any suggestion or help.
> >=20
> > Cheers,
> >=20
> > -----------------------
> > Alan Wilter S. da Silva
> > -----------------------
> > Laborat=F3rio de F=EDsica Biol=F3gica
> > Instituto de Biof=EDsica Carlos Chagas Filho
> > Universidade do Brasil/UFRJ
> > Rio de Janeiro, Brasil
> >=20
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the=20
> > www interface or send it to gmx-users-request at gromacs.org.
> >=20
>--=20
>Groeten, David.
>________________________________________________________________________
>Dr. David van der Spoel, Dept. of Cell & Mol. 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
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>--__--__--
>
>Message: 14
>From: nanyu101 <nanyu101 at sina.com>
>To: gmx-users at gromacs.org
>Date: Tue, 15 Apr 2003 16:55:24 +0800
>Subject: [gmx-users] RB dihedral again and dihedral constants
>Reply-To: gmx-users at gromacs.org
>
>Dear Dr.David,
> Thanks for your prompt reply.I have known there are many parameters for
> RB dihedral type in OPLS.But if I want to simulate my system in ffG43a2
> force field, where should I put these force constants that I have already
> fitted them ourselves.
> By the way,I have met something very interesting when I try to
> understand how the torsion parameters work. I have done as follows:
>1.I have changed all the dihedral force constants to zero and run energy
>minimization of my system,the Gromacs give me the same results as before I
>have changed the dihedral force constant. Do you know what has happened?
>2.Firstly,I think that Gromacs has not read ffG43a2bond.itp file,so I have
>change one bond constant to zero,the result changed.Now,we can conclude
>that Gromacs has read ffG43a2bond.itp file,but why didn't it read the
>dihedral part?
> Do Gromacs do some special operation when the force constant is zero?
>Thanks for your help and any comment is appreciated.
>
>Best wishes,
>Xianhui Wu
>______________________________________
>
>===================================================================
>
>--__--__--
>
>Message: 15
>Date: Mon, 14 Apr 2003 08:09:11 +0200
>From: Anton Feenstra <feenstra at chem.vu.nl>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] how to prove the charges in rtp file!
>Reply-To: gmx-users at gromacs.org
>
>nanyu101 wrote:
> > Dear gmx-users,
> > I have done some simulation for a polyester and generated its rtp
> file myself.Some of partial charges in my residue were from a reference
> literature.Because I do it for a polyester, I should prove it firstly
> with ab initio results.I try to do it as follows:
>[...]
>
>Dear Xianhui,
>
>
>The answer to your question is actually a whole area of reasearch:
>force field development. Energies you get from MD or after energy
>minimizations are generally *not* comparable to single point energies
>from Quantum calculations, and the same goes for energy differences.
>In MD/EM the energy is simply the sum of all pairwise interactions
>as defined in the forcefield. In QM, the energy is actually a
>physical property of the molecule.
>
>For e.g. liquids (DMSO, water), the first things to optimize when
>adjusting forcefield parameters, are density and heat of vaporization.
>Internal parameters (bond lengths and angles), are usually taken from
>crystal structures, or directly from QM calculations. For polymers,
>I am not sure how best to do it, but you should be able to find some
>literature about this... If your polymer will be solvated, be sure
>also to get the solvation (free) energy of the monomers correct.
>
>As for charges, in the Gromacs & Gromos forcefields, these are taken
>more or less as adustable parameters. Usually they are about half of
>the charge you would get from QM calculations, but it depends. Things
>like density, hydrogen bond strength etc. depend on the charge.
>
>If the minimized structure you get out of your EM is not what it
>should be, check the angle and dihedral parameters first. But also
>charges might have a (big) effect; sometimes you may have to exclude
>internal charge-charge interactions (by adding an explicit [exclusions]
>section to your .rtp or .top), or you may have to adjust the charges
>themselves.
>
>Hope this gets you going for a bit!
>
>--
>Groetjes,
>
>Anton
> _____________ _______________________________________________________
>| | |
>| _ _ ___,| K. Anton Feenstra |
>| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
>|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
>| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
>| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
>| | "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
>
>
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