[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
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> 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!
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>
> ------------------------------
>
> 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
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