[gmx-users] Re: gmx-users Digest, Vol 60, Issue 89
Anirban Ghosh
anirbanz83 at yahoo.co.in
Thu Apr 16 06:14:14 CEST 2009
Hi,
Thanks for the reply.
I converted the .dcd file to .trr format using the catdcd program. I used the command " g_covar -f TOTAL_50MS.trr -s CG_TNF.pdb -n new.ndx -o eigenval.xvg -v eigenvec.trr" to run and getting the error as follows:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Warning double different entries ASN ND 16.0227 and 144.24 on line 134 in file atommass.dat
Using last entry (16.0227)
Warning double different entries GLN NE 16.0227 and 20.1797 on line 140 in file atommass.dat
Using last entry (16.0227)
Warning double different entries HISA NE 14.0067 and 16.0227 on line 144 in file atommass.dat
Using last entry (14.0067)
Warning double different entries HISB ND 14.0067 and 16.0227 on line 145 in file atommass.dat
Using last entry (14.0067)
Warning double identical entries for HIS1 NE 14.0067 on line 146 in file atommass.dat
Entries in atommass.dat: 173
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Choose a group for the least squares fit
Group 0 ( System) has 45 elements
Group 1 ( TA) has 15 elements
Group 2 ( TB) has 15 elements
Group 3 ( TC) has 15 elements
Group 4 (a_15_a_30_a_45) has 3 elements
Select a group: 0
Selected 0: 'System'
Choose a group for the covariance analysis
Group 0 ( System) has 45 elements
Group 1 ( TA) has 15 elements
Group 2 ( TB) has 15 elements
Group 3 ( TC) has 15 elements
Group 4 (a_15_a_30_a_45) has 3 elements
Select a group: 0
Selected 0: 'System'
Note: the fit and analysis group are identical,
while the fit is mass weighted and the analysis is not.
Making the fit non mass weighted.
Calculating the average structure ...
Segmentation fault
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
I also edited the aminoacids.dat file by giving the CG Beads names there. Do I need to incorporate any other change?
Regards,
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
________________________________
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Today's Topics:
1. Re: Implicit Solvent System - Energy Minimization (Mark Abraham)
2. g_covar Segmentation fault (Anirban Ghosh)
3. Re: g_covar Segmentation fault (Mark Abraham)
4. Re: g_covar Segmentation fault (Nicolas)
5. Topologies and charges for large organic ligands (Dean Cuebas)
6. Re: Topologies and charges for large organic ligands
(Ran Friedman)
7. Problem with grompp? (Hoof, B. van)
----------------------------------------------------------------------
Message: 1
Date: Wed, 15 Apr 2009 19:55:26 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] Implicit Solvent System - Energy Minimization
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <49E5AF0E.6020503 at anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Grace Tang wrote:
> Hello All,
>
> I am doing energy minimization on a protein crystal structure to relax
> it. Afterwards, I plan to run md simulation with implicit solvent. I
> am new at this and have many questions.
> 1. Should the implicit solvent conditions be enabled when I run the
> energy minimization?
No - while GROMACS has some vestiges in the user interface of an earlier
attempt to implement implicit solvation simulations, these will not
functional until at least version 4.1.
> 2. What minimum potential energy should I expect (i know that when
> explicit water is present, the energy often reaches -10E5 or -10E6)
Negative, and vaguely proportional to the number of atoms.
> 3. What kind of emtol is appropriate? Is it better to set it high so
> that the system converges, or is it okay if machine precision is reached.
It's pretty much irrelevant for preparing a system for MD. You'll have
to equilibrate it later, and the value of an EM step is merely relieving
any bad atom-atom contacts before they turn into huge accelerations. If
the equilibration doesn't crash, you did enough EM.
Mark
> Below are 2 example runs I did with implicit_solvent = no
> When I decreased the step size, the system did not converge anymore. I
> was wondering if this was due to chance, precision issues (I am using
> single precision), or perhaps the emstep = 0.1 was reaching a nearby
> minimum and 0.01 was reaching the local minimum. Note, maximum force
> gets rather large when convergence is to machine precision.
>
> emtol = 1000
> emstep = 0.1
> Steepest Descents converged to Fmax < 1000 in 29 steps
> Potential Energy = -4.9613008e+003
> Maximum force = 6.4596338e+002 on atom 235
> Norm of force = 1.0625026e+002
>
> emtol = 1000
> emstep = 0.01
> Steepest Descents converged to machine precision in 25 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy = -3.9642480e+003
> Maximum force = 5.1200122e+003 on atom 416
> Norm of force = 3.6602789e+002
>
> Any advice is greatly appreciated. Much thanks!
> - Grace
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
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> Please search the archive at http://www.gromacs.org/search before posting!
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------------------------------
Message: 2
Date: Wed, 15 Apr 2009 18:12:32 +0530 (IST)
From: Anirban Ghosh <anirbanz83 at yahoo.co.in>
Subject: [gmx-users] g_covar Segmentation fault
To: GROMACS <gmx-users at gromacs.org>
Message-ID: <1093.26419.qm at web8504.mail.in.yahoo.com>
Content-Type: text/plain; charset="utf-8"
Hi ALL,
I have a system of beads with which I ran a CGMD (coarse grained MD) using NAMD. Now I want to do a PCA analysis of this system using GROMACS. So I converted the trajectory in .trr format and made an index file of the entire system (45 beads). But now when I try to run g_covar using the group consisting the entire system, for least square fit and covariance analysis, it is giving Segmentation Fault. Am I doing anything wrong. Any suggestion is welcome.
Regards,
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
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Message: 3
Date: Wed, 15 Apr 2009 22:48:51 +1000
From: Mark Abraham <Mark.Abraham at anu.edu.au>
Subject: Re: [gmx-users] g_covar Segmentation fault
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <49E5D7B3.3030305 at anu.edu.au>
Content-Type: text/plain; charset=UTF-8; format=flowed
Anirban Ghosh wrote:
> Hi ALL,
>
> I have a system of beads with which I ran a CGMD (coarse grained MD)
> using NAMD. Now I want to do a PCA analysis of this system using
> GROMACS. So I converted the trajectory in .trr format and made an index
> file of the entire system (45 beads). But now when I try to run g_covar
> using the group consisting the entire system, for least square fit and
> covariance analysis, it is giving Segmentation Fault. Am I doing
> anything wrong. Any suggestion is welcome.
Yes you're doing something wrong, but if you don't tell us at least your
command line and your full output, how might we be expected to help? :-)
Mark
------------------------------
Message: 4
Date: Wed, 15 Apr 2009 15:02:55 +0200
From: Nicolas <nsapay at ucalgary.ca>
Subject: Re: [gmx-users] g_covar Segmentation fault
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <49E5DAFF.2000705 at ucalgary.ca>
Content-Type: text/plain; charset="utf-8"
Anirban Ghosh a écrit :
> Hi ALL,
>
> I have a system of beads with which I ran a CGMD (coarse grained MD)
> using NAMD. Now I want to do a PCA analysis of this system using
> GROMACS. So I converted the trajectory in .trr format
Convert a dcd file into a trr file is not that straightforward. How did
you do that?
> and made an index file of the entire system (45 beads). But now when I
> try to run g_covar using the group consisting the entire system, for
> least square fit and covariance analysis, it is giving Segmentation
> Fault. Am I doing anything wrong. Any suggestion is welcome.
You probably also need a tpr file. To create it, you need the parameters
of your force field (in Gromacs format), the topology of each molecule
you've got in your system (still in Gromacs format) and to run grompp.
Depending on the original format of your force field, in can be quite
difficult to do the file format conversion.
Hope that helps...
Nicolas
>
> Regards,
>
>
> *Anirban Ghosh*
> *Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
> *
>
>
> ------------------------------------------------------------------------
> Add more friends to your messenger and enjoy! Invite them now.
> <http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/>
>
> ------------------------------------------------------------------------
>
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------------------------------
Message: 5
Date: Wed, 15 Apr 2009 10:03:40 -0500
From: Dean Cuebas <deancuebas at missouristate.edu>
Subject: [gmx-users] Topologies and charges for large organic ligands
To: <gmx-users at gromacs.org>
Message-ID: <C60B617C.28718%deancuebas at missouristate.edu>
Content-Type: text/plain; charset="US-ASCII"
Dear colleagues,
In 53a6, the topology and charges for (NAD+) nicotinamide adenine
dinucleotide are present (listed as NADH, 52 atoms) in polar hydrogen form
(without aromatic hydrogens).
Is there anyone who can tell me how such a molecule was charge group
parameterized? (with sufficient certainty to be included in the ff).
Please understand that I am not asking how to use the NAD topology that's
provided.
I've read that prodrg is a "good starting point" for parametrizing a ligand,
but what is the path to "improving" such a ligand from that starting point?
(the provided topology for NAD+ in the ff shows 17 charge groups with
an average of 3-4 atoms per charge group, whereas prodrg gives only 11
charge groups.)
I'm not concerned about angles and dihedrals, since that is pretty
painless... it's the charge groups that I'm concerned about.
In a nutshell, who and how was the final NAD+ parameters decided upon??
Does anyone know this?? Is it simply chemical intuition of estimated
charges that reproduce the dipole of the moiety (like an adenine ring), and
the charge groups contain the minimum number of atoms that reflect this?
Is there an algorithm to generating "improved" charge groups?
I ask these questions because my ligands are large organics... MW 800 and
greater.
Thanks for any and all help in this regard.
--
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas at smsu.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Southwest Missouri State University
Springfield, Missouri 65804
------------------------------
Message: 6
Date: Wed, 15 Apr 2009 17:26:50 +0200
From: Ran Friedman <r.friedman at bioc.uzh.ch>
Subject: Re: [gmx-users] Topologies and charges for large organic
ligands
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <49E5FCBA.10606 at bioc.uzh.ch>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
The answer is (or should be) in:
@article{Oostenbrink2004,
Author = {Oostenbrink, C. and Villa, A. and Mark, A. E. and Van
Gunsteren, W. F.},
Title = {A biomolecular force field based on the free enthalpy of
hydration and solvation: The GROMOS force-field parameter sets 53A5 and
53A6},
Journal = {J. Comput. Chem.},
Volume = {25},
Pages = {1656-1676},
Year = {2004} }
Good luck,
Ran.
Dean Cuebas wrote:
> Dear colleagues,
>
> In 53a6, the topology and charges for (NAD+) nicotinamide adenine
> dinucleotide are present (listed as NADH, 52 atoms) in polar hydrogen form
> (without aromatic hydrogens).
>
> Is there anyone who can tell me how such a molecule was charge group
> parameterized? (with sufficient certainty to be included in the ff).
>
> Please understand that I am not asking how to use the NAD topology that's
> provided.
>
> I've read that prodrg is a "good starting point" for parametrizing a ligand,
> but what is the path to "improving" such a ligand from that starting point?
> (the provided topology for NAD+ in the ff shows 17 charge groups with
> an average of 3-4 atoms per charge group, whereas prodrg gives only 11
> charge groups.)
>
> I'm not concerned about angles and dihedrals, since that is pretty
> painless... it's the charge groups that I'm concerned about.
>
> In a nutshell, who and how was the final NAD+ parameters decided upon??
> Does anyone know this?? Is it simply chemical intuition of estimated
> charges that reproduce the dipole of the moiety (like an adenine ring), and
> the charge groups contain the minimum number of atoms that reflect this?
>
> Is there an algorithm to generating "improved" charge groups?
>
> I ask these questions because my ligands are large organics... MW 800 and
> greater.
>
> Thanks for any and all help in this regard.
>
>
------------------------------
Message: 7
Date: Wed, 15 Apr 2009 17:25:15 +0200
From: "Hoof, B. van" <B.v.Hoof at tue.nl>
Subject: [gmx-users] Problem with grompp?
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
<C33253DAA8B7D24E9523B6F1DF162F5A01A73BE9BCDE at EXCHANGE10.campus.tue.nl>
Content-Type: text/plain; charset="us-ascii"
Hi everyone,
Since I am a new user of Gromacs, this problem is probably rather trivial, but I hope one of you would like to help me nonetheless. I have created a starting structure in a not very optimal situation, which I have then minimized. To continue, I would like to equilibrate the system further using leap-frog MD. To do so, I have used grompp in the following way:
grompp -f martini_md1.mdp -c minimized.gro -p martini.top -maxwarn 10
This creates the following mdout.mdp: see attachment
Now as far as I can see, using the command `mdrun -v -c md_run.gro' should result in performing a 1,000,000 iteration md simulation of this system. However, when I issue that command, instead what I get is this:
>>>
:-) G R O M A C S (-:
Good ROcking Metal Altar for Chronical Sinners
:-) VERSION 4.0.4 (-:
[...]
:-) mdrun (-:
Option Filename Type Description
------------------------------------------------------------
[...]
Getting Loaded...
Reading file topol.tpr, VERSION 4.0.4 (single precision)
Loaded with Money
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 10000
Step= 1, Dmax= 1.0e-02 nm, Epot= 1.23314e+20 Fmax= 2.04950e+19, atom= 11163
Step= 2, Dmax= 1.2e-02 nm, Epot= 5.22616e+17 Fmax= 2.22256e+20, atom= 10863
Step= 3, Dmax= 1.4e-02 nm, Epot= 1.46382e+17 Fmax= 7.52962e+17, atom= 10593
Step= 4, Dmax= 1.7e-02 nm, Epot= 1.21703e+17 Fmax= 3.72098e+16, atom= 10331
Step= 5, Dmax= 2.1e-02 nm, Epot= 2.22862e+16 Fmax= 4.87326e+18, atom= 10857
Step= 6, Dmax= 2.5e-02 nm, Epot= 1.09032e+16 Fmax= 4.39937e+15, atom= 15106
Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81517e+15 Fmax= 6.07049e+14, atom= 15230
Step= 8, Dmax= 3.6e-02 nm, Epot= 2.84750e+14 Fmax= 9.82848e+14, atom= 14675
Step= 9, Dmax= 4.3e-02 nm, Epot= 2.33131e+14 Fmax= 2.39469e+13, atom= 11419
Step= 10, Dmax= 5.2e-02 nm, Epot= 7.23189e+12 Fmax= 2.72305e+14, atom= 14565
Step= 11, Dmax= 6.2e-02 nm, Epot= 3.19510e+12 Fmax= 4.82192e+12, atom= 10638
Step= 13, Dmax= 3.7e-02 nm, Epot= 1.82616e+12 Fmax= 1.11184e+13, atom= 11929
[... etc.....]
<<<
This is a minimization using the steepest descent algorithm. What am I doing wrong here?
Thank you in advance for your kind help!
Greetings,
Bram van Hoof
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