[gmx-users] Re: gmx-users Digest, Vol 101, Issue 52

Praveen Kumar Sappidi ch11d033 at smail.iitm.ac.in
Tue Sep 18 15:09:56 CEST 2012


Dr Justin
This is my Topolofy file for Ethanol
[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB   
chargeB      massB
     1          H      1   ETHH     EH      1      0.408      1.008   ; qtot 0.408
     2         OA      1   ETHH     EO      1     -0.674    15.9994   ; qtot
-0.266
     3        CH2      1   ETHH    EC1      1      0.266     14.027   ; qtot 0
     4        CH3      1   ETHH    EC2      2          0     15.035   ; qtot 0

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     2    gb_1
    2     3     2    gb_18
    3     4     2    gb_27

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     4     1 

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    1     2     3     2    ga_12
    2     3     4     2    ga_15

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2      
     c3            c4            c5
    1     2     3     4     1    gd_23

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include ethanol topology
#include "ethanol.itp"


; Include water topology
#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif



; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
GROwing Monsters And Cloning Shrimps in water

[ molecules ]
; Compound        #mols
Protein             1
ETHH             1852
SOL              4000
On Tue, 18 Sep 2012 15:00:07 +0200 (CEST), gmx-users-request wrote
> Send gmx-users mailing list submissions to
> 	gmx-users at gromacs.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> 	gmx-users-request at gromacs.org
> 
> You can reach the person managing the list at
> 	gmx-users-owner at gromacs.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
> 
> Today's Topics:
> 
>    1. Hbond-ETH-WATER (Praveen Kumar  Sappidi)
>    2. Re: charge calculation........ (tarak karmakar)
>    3. why traj.trr appears (Dr. Vitaly Chaban)
>    4. Re: Hbond-ETH-WATER (Justin Lemkul)
>    5. Re: why traj.trr appears (Justin Lemkul)
>    6. Re: LINCS warning in md run
>       (reisingere at rostlab.informatik.tu-muenchen.de)
>    7. Re: Hbond-ETH-WATER (Justin Lemkul)
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 18 Sep 2012 18:38:41 +0630
> From: "Praveen Kumar  Sappidi" <ch11d033 at smail.iitm.ac.in>
> Subject: [gmx-users] Hbond-ETH-WATER
> To: gmx-users at gromacs.org
> Message-ID: <20120918120320.M14128 at smail.iitm.ac.in>
> Content-Type: text/plain;	charset=utf-8
> 
> Hi all
>  Am Simulating Ethanol-water system using Gromacs4.0.7
>  the problem is am not able to calculate number of hydrogen bonds in 
> ethanol and water-ethanol. i can see a small peak at 0.24 of Ethanol-
> water RDFs and visually also i can see hydrogen bonding is formed
> 
>   am using command g_hbond -f *.xtc -s *.tpr -n *.ndx -num .xvg
> 
>  please help if anyone knows the solution
> --
> Thanks & Regards
> Praveenkumar Sappidi
> Research Scholar
> Molecular modelling and simulation lab
> Chemical Engineering Department
> IIT Madras-600036
> Chennai,INDIA
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 18 Sep 2012 17:41:31 +0530
> From: tarak karmakar <tarak20489 at gmail.com>
> Subject: Re: [gmx-users] charge calculation........
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<CAGZMOotW6jkd6rZGbodKjEBZyM67D9ejGApRjHnru8N27yZyZQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Thanks Mark.
> 
> I have gone through the link "Parameterization of novel molecules" 
> and I see quantum calculations can be handy for this type of charge 
> calculation (AMBER). So for the unprotonated tyrosine, I am taking 
> two more amino acids (left and right) and calculating ESP charges of 
> the tri-peptide by using HF / 6-31(+)g(d) level of theory. Can you please
> tell me whether I can include the partial charges of all the atoms of
> the middle tyrosine (unprotonated) in the aminoacids.rtp file to
> simulate the protein ?
> 
> Thanks,
> Tarak
> 
> On Mon, Sep 17, 2012 at 6:21 PM, Mark Abraham 
> <Mark.Abraham at anu.edu.au> wrote:
> > On 17/09/2012 10:01 PM, tarak karmakar wrote:
> >>
> >> Dear All,
> >>
> >>               I want to have one of tyrosine residues in my protein to
> >> be unprotonated. I am using amber force field for the simulation. But
> >> in aminoacid.rtp there is no entry for the unprotonated one. So I am
> >> adding it by myself in to the .rtp file. Now I am bit confused with
> >> the charge of the unprotonated one. How can I calculate the partial
> >> charges for each and every atoms in  unprotonated tyrosine? Would
> >> Gaussian/SCF be a good one to deal with this matter? Should I take the
> >> tyrosine amino acid alone to calculate the charge in Gaussian ?
> >> Please suggest me the proper method(s) to calculate the charge.
> >
> >
> > It varies, but should be determined by the process by which the rest of the
> > force field was determined. See
> > http://www.gromacs.org/Documentation/How-tos/Parameterization
> >
> > Mark
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
> 
> ------------------------------
> 
> Message: 3
> Date: Tue, 18 Sep 2012 14:29:23 +0200
> From: "Dr. Vitaly Chaban" <vvchaban at gmail.com>
> Subject: [gmx-users] why traj.trr appears
> To: gmx-users at gromacs.org
> Message-ID:
> 	<CAPXdD+bmndF0Mt-ssf7Nq9C5C-BOz+ipibZvErUZT=2qOTF55A at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Dear All -
> 
> I an using the current version of gromacs. Although I have
> 
> nstxout                  = 0
> nstvout                  = 0
> nstfout                  = 0
> 
> in the MDP file, the traj.trr file appears during the MD run (and is
> quite large). In older versions, there was no traj.trr with such an
> input.
> 
> Did I miss something, please?
> 
> Dr. Vitaly V. Chaban, 430 Hutchison Hall
> Dept. Chemistry, University of Rochester
> 120 Trustee Road, Rochester, NY 14627-0216
> THE UNITED STATES OF AMERICA
> 
> ------------------------------
> 
> Message: 4
> Date: Tue, 18 Sep 2012 08:28:17 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Hbond-ETH-WATER
> To: ch11d033 at smail.iitm.ac.in,	Discussion list for GROMACS users
> 	<gmx-users at gromacs.org>
> Message-ID: <505868E1.4050901 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> On 9/18/12 8:08 AM, Praveen Kumar Sappidi wrote:
> > Hi all
> >   Am Simulating Ethanol-water system using Gromacs4.0.7
> >   the problem is am not able to calculate number of hydrogen bonds in ethanol
> > and water-ethanol.
> >   i can see a small peak at 0.24 of Ethanol-water RDFs and visually also i can
> > see hydrogen bonding is formed
> >
> >    am using command g_hbond -f *.xtc -s *.tpr -n *.ndx -num .xvg
> >
> >   please help if anyone knows the solution
> 
> You haven't described why the above command failed to produce what 
> you wanted. g_hbond should prompt you to choose groups, which should 
> include ethanol and water, so you can create plots of ethanol-
> ethanol, water-water, and ethanol-water hydrogen bonds.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> ------------------------------
> 
> Message: 5
> Date: Tue, 18 Sep 2012 08:43:16 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] why traj.trr appears
> To: vvchaban at gmail.com,	Discussion list for GROMACS users
> 	<gmx-users at gromacs.org>
> Message-ID: <50586C64.8020500 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> On 9/18/12 8:29 AM, Dr. Vitaly Chaban wrote:
> > Dear All -
> >
> > I an using the current version of gromacs. Although I have
> >
> > nstxout                  = 0
> > nstvout                  = 0
> > nstfout                  = 0
> >
> > in the MDP file, the traj.trr file appears during the MD run (and is
> > quite large). In older versions, there was no traj.trr with such an
> > input.
> >
> > Did I miss something, please?
> >
> 
> The above combination should turn off production of a .trr file. 
>  Something doesn't add up.  Verify your settings in the .log and/or 
> .tpr file - perhaps you've mixed up .mdp files.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> ------------------------------
> 
> Message: 6
> Date: Tue, 18 Sep 2012 14:58:41 +0200
> From: reisingere at rostlab.informatik.tu-muenchen.de
> Subject: Re: [gmx-users] LINCS warning in md run
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID: <f2e9b5cfb5297c858d42968f1871b0bd.squirrel at rostlab.org>
> Content-Type: text/plain;charset=iso-8859-1
> 
> Okey,
>  now I tried it without any fixed residues. But still the energy 
> after the minimization is not very low and I still get the LINCS warnings.
> 
> The mdp file I use for the minimization looks like this:
> 
> define                  = -DPOSRES
> integrator              = steep
> emtol                   = 10
> nsteps                  = 1500
> nstenergy               = 1
> energygrps              = System
> coulombtype             = PME
> rcoulomb                = 0.9
> rvdw                    = 0.9
> rlist                   = 0.9
> fourierspacing          = 0.12
> pme_order               = 4
> ewald_rtol              = 1e-5
> pbc                     = xyz
> 
> the mdp file for the md run looks like this:
> 
> define          = -DPOSRES
> integrator              = md
> dt                      = 0.001
> nsteps          = 5000
> nstxout         = 100
> nstvout         = 0
> nstfout         = 0
> nstlog          = 1000
> nstxtcout               = 500
> nstenergy               = 5
> energygrps              = Protein Non-Protein
> nstcalcenergy   = 5
> nstlist         = 10
> ns-type         = Grid
> pbc                     = xyz
> rlist           = 0.9
> coulombtype             = PME
> rcoulomb                = 0.9
> rvdw            = 0.9
> fourierspacing          = 0.12
> pme_order               = 4
> ewald_rtol              = 1e-5
> gen_vel         = yes
> gen_temp                = 200.0
> gen_seed                = 9999
> constraints             = all-bonds
> tcoupl          = V-rescale
> tc-grps         = Protein  Non-Protein
> tau_t           = 0.1     0.1
> ref_t           = 298     298
> pcoupl          = no
> 
> The output of the minimization run is:
> 
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy  = -7.9280412e+05
> Maximum force     =  1.0772942e+04 on atom 979
> Norm of force     =  9.6685356e+01
> 
> The output of the MD run is:
> 
> Step 1031, time 1.031 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.001431, max 0.010707 (between atoms 976 and 979)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     976    979   81.6    0.1272   0.0970      0.0960
> 
> The atom 979 is the hydrogen atom on the phosphate. There has to be one
> hydrogen atoms because it is protonated once. The other atom 976 is the
> oxygen atom where the hydrogen atom is bound to.
> The bounding parameters for this kind of binding were already there. 
> I didn't add them.
> 
> I already did it for another phosphorylation on another position in this
> structure. And here I also got many LINCS errors. And again the 
> problem is the connection between the hydrogen atom and the oxygen atom.
> 
> But I do not understand why.
> Can you please help me?!
> >
> >
> > On 9/18/12 7:22 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> >> I need the rest of the structure just as it is now because I want to do
> >> electrostatic analysis with it.
> >
> > Another thing worth considering - why do you necessarily need the rest of
> > the
> > structure to be identical?  Or perhaps better stated, why do you believe
> > this to
> > be the more appropriate model of reality?  Phosphorylation events
> > frequently
> > trigger structural changes in the protein, so I see no reason to assume it
> > will
> > have no effect on the rest of the structure.  At the very least, you can
> > try a
> > "normal" EM and MD procedure without freezing anything to see if you can
> > determine the problem.  If things run normally without freezing, then you
> > know
> > that whatever you are doing here is artificial and problematic.
> >
> > -Justin
> >
> >> I just added the phosphate manually and so I want to minimize and run a
> >> short MD with it.
> >>
> >> I added the dihedraltype of the amber database
> >>
(http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p)
> >> to the ffbonded file.
> >> And additionally I looked at the protein and made all the residues which
> >> could somehow influence the protein flexible so that eventual clashes
> >> can
> >> be repaired.
> >> But still I got the error:
> >>
> >> ..Step 3612, time 3.612 (ps)  LINCS WARNING
> >> relative constraint deviation after LINCS:
> >> rms 0.000008, max 0.000031 (between atoms 975 and 978)
> >> bonds that rotated more than 30 degrees:
> >>   atom 1 atom 2  angle  previous, current, constraint length
> >>      976    979   32.6    0.0961   0.0960      0.0960
> >>
> >> Step 3613, time 3.613 (ps)  LINCS WARNING
> >> relative constraint deviation after LINCS:
> >> rms 0.000237, max 0.001400 (between atoms 976 and 979)
> >> bonds that rotated more than 30 degrees:
> >>   atom 1 atom 2  angle  previous, current, constraint length
> >>      976    979   33.4    0.0960   0.0959      0.0960
> >> ..
> >>
> >> Too many LINCS warnings (1000)
> >>
> >>
> >> I already minimized the protein and everything was fine. There were no
> >> errors:
> >>
> >> Steepest Descents converged to machine precision in 15 steps,
> >> but did not reach the requested Fmax < 10.
> >> Potential Energy  = -7.7436938e+05
> >> Maximum force     =  8.6871973e+03 on atom 979
> >> Norm of force     =  7.1224258e+01
> >>
> >> gcq#49: "You Could Make More Money As a Butcher" (F. Zappa)
> >>
> >>
> >> Steepest Descents converged to machine precision in 15 steps,
> >> but did not reach the requested Fmax < 10.
> >> Potential Energy  = -7.7436938e+05
> >> Maximum force     =  8.6871973e+03 on atom 979
> >> Norm of force     =  7.1224258e+01
> >>
> >>
> >> And also during the grompp run there are no errors.
> >> Can you please help me to find out where the problem lies?
> >>
> >>
> >> Thank you,
> >>   Eva
> >>
> >>
> >>>
> >>>
> >>> On 9/13/12 5:50 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> >>>> Ah okey. Thank you.
> >>>> I will write them.
> >>>>
> >>>> Hmm, but the protein is a crystal structure from pdb with a resolution
> >>>> of
> >>>> 1.2. I already added the hydrogen atoms to this structure and there I
> >>>> already minimized them and made a md run. And there were no errors.
> >>>> And
> >>>> now I only added the phosphate to the minimized structure. So I
> >>>> thought
> >>>> that I only had to minimize the phosphate and the residue it bound on.
> >>>> Or is there a mistake in my thought here?
> >>>
> >>> If adding the phosphate resulted in a crash, then clearly that's the
> >>> problem.  I
> >>> don't understand why you would run EM on just the phosphate and keep
> >>> the
> >>> rest of
> >>> the protein structure frozen.  Again, that potentially prevents clashes
> >>> from
> >>> being resolved.  I don't understand what value there is in only
> >>> minimizing
> >>> the
> >>> phosphate.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ========================================
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Research Scientist
> >>> Department of Biochemistry
> >>> Virginia Tech
> >>> Blacksburg, VA
> >>> jalemkul[at]vt.edu | (540) 231-9080
> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>>
> >>> ========================================
> >>> --
> >>> gmx-users mailing list    gmx-users at gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
> >>>
> >>
> >>
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
> >
> 
> ------------------------------
> 
> Message: 7
> Date: Tue, 18 Sep 2012 08:58:08 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Hbond-ETH-WATER
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <50586FE0.5010905 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> On 9/18/12 8:56 AM, Praveen Kumar Sappidi wrote:
> > Hi Justin
> > prompt for calculation i have shown below
> >
> >   Reading file eth-water60%-production.tpr, VERSION 4.0.7 (single precision)
> > Note: tpx file_version 58, software version 73
> > Specify 2 groups to analyze:
> > Group     0 (         System) has 19412 elements
> > Group     1 (           ETHH) has  7412 elements
> > Group     2 (            SOL) has 12000 elements
> > Group     3 (            EC1) has  1853 elements
> > Group     4 (            EC2) has  1853 elements
> > Group     5 (             EO) has  1853 elements
> > Group     6 (             OW) has  4000 elements
> > Group     7 (             EH) has  1853 elements
> > Group     8 (            HW1) has  4000 elements
> > Group     9 (            HW2) has  4000 elements
> > Select a group: 1
> > Selected 1: 'ETHH'
> > Select a group: 2
> > Selected 2: 'SOL'
> > Checking for overlap in atoms between ETHH and SOL
> > Calculating hydrogen bonds between ETHH (7412 atoms) and SOL (12000 atoms)
> > Found 4000 donors and 4000 acceptors
> > Reading frame       0 time    0.000
> > Will do grid-seach on 15x15x15 grid, rcut=0.35
> > Reading frame    2000 time 4000.000
> > Average number of hbonds per timeframe 0.000 out of 8e+06 possible
> >
> 
> Can you please post your topology for ethanol?  I suspect your atoms 
> are named in a way that g_hbond doesn't not recognize, since the 
> number of donors and acceptors seem to only correspond to water 
> (12000/3 = 4000).
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> ------------------------------
> 
> -- 
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> 
> End of gmx-users Digest, Vol 101, Issue 52
> ******************************************


--
Thanks & Regards
Praveenkumar Sappidi
Research Scholar
Molecular modelling and simulation lab
Chemical Engineering Department
IIT Madras-600036
Chennai,INDIA




More information about the gromacs.org_gmx-users mailing list