[gmx-users] how can we modify *.rtp file? (again)
marzieh dehghan
dehghanmarzieh at gmail.com
Thu Jan 22 16:40:12 CET 2015
Thank you, for your nice and prompt reply, however we had studied the
following articles
1.
Practical Considerations for Building GROMOS-Compatible Small-Molecule
Topologies
2.
A Biomolecular Force Field Based on the Free Enthalpy of Hydration and
Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6.
But there was some inconsistency, your reply solved them but now we have
few questions:
1.
Since we created covalent bond between glucose and insulin, Should we
consider Glucose as a reagent in residuetype.dat?
2.
In the ffbonded.itp, Are CA and CHn same components?
3.
Do the bonds between C-O (single or double bond) include in gb_4?
4.
What's the meaning of OA and OM?
thanks a lot
On Thu, Jan 22, 2015 at 6:00 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. recovering topology from tpr (Rebeca Garc?a Fandi?o)
> 2. Re: QM/MM excited state optimization (xiao)
> 3. Re: recovering topology from tpr (Mark Abraham)
> 4. how can we modify *.rtp file? (marzieh dehghan)
> 5. Re: how can we modify *.rtp file? (Justin Lemkul)
> 6. constant pH simulations in GROMACS 4.5 (Sahithya S Iyer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 22 Jan 2015 11:11:51 +0000
> From: Rebeca Garc?a Fandi?o <regafan at hotmail.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] recovering topology from tpr
> Message-ID: <DUB115-W81C34D2B2B16E7A8282DC1B7490 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Gromacs users,
> Is it posible to recover the topology files (itp or top) from a binary tpr
> file?
>
> I have tried using this script:
>
>
> https://pythonhosted.org/MDAnalysis/_modules/MDAnalysis/topology/TPRParser.html
>
> However, the itp file seems a single line like this:
>
> {'_bonds':
> [(0, 3), (0, 7), (0, 11), (0, 13), (0, 74), (0, 80), (1, 4), (1, 6),
> (1, 10), (1, 14), (1, 75), (2, 5), (2, 11), (2, 15), (2, 16), (2, 76),
> (3, 6), (3, 12), (3, 14), (3, 17), (3, 21), (4, 5), (4, 11), (4, 13),
> (4, 18), (4, 22), (4, 24), (5, 8), (5, 9), (5, 12), (5, 75), (6, 11),
> (6, 76), (7, 10), (10, 13), (10, 16), (10, 76), (16, 19), (16, 23), (16,
> 25), (16, 27), (17, 20), (17, 22), (17, 24), (17, 28), (18, 21), (18,
> 25), (18, 29), (18, 30), (19, 22), (19, 26), (19, 28), (19, 31), (19,
> 35), (20, 21), (20, 25), (20, 27), (20, 32), (20, 36), (20, 38), (21,
> 26), (22, 25), (23, 24), (24, 27), (24, 30), (30, 33), (30, 37), (30,
> 39), (30, 41), (31, 34), (31, 36), (31, 38), (31, 42), (32, 35), (32,
> 39), (32, 43), (32, 44), (33, 36), (33, 40), (33, 42), (33, 45), (33,
> 49), (34, 35), (34, 39), (34, 41), (34, 46), (34, 50), (34, 52), (35,
> 40), (36, 39), (37, 38), (38, 41), (38, 44), (44, 47), (44, 51), (44,
> 53), (44, 55), (45, 48), (45, 50), (45, 52), (45, 56), (46, 49), (46,
> 53), (46, 57), (46, 58), (47, 50), (47, 54), (47, 56), (47, 59), (47,
> 63), (48, 49), (48, 53), (48, 55), (48, 60), (48, 64), (48, 66), (49,
> 54), (50, 53), (51, 52), (52, 55), (52, 58), (58, 61), (58, 65), (58,
> 67), (58, 69), (59, 62), (59, 64), (59, 66), (59, 70), (60, 63), (60,
> 67), (60, 71), (60, 72), (61, 64), (61, 68), (61, 70), (61, 73), (61,
> 77), (62, 63), (62, 67), (62, 69), (62, 74), (62, 78), (62, 80), (63,
> 68), (64, 67), (65, 66), (66, 69), (66, 72), (72, 75), (72, 79), (72,
> 81), (72, 83), (73, 76), (73, 78), (73, 80), (73, 84), (74, 77), (74,
> 81), (74, 85), (75, 78), (75, 82), (75, 84), (76, 77), (76, 81), (76,
> 83), (77, 82), (78, 81), (79, 80), (80, 83)], '_dihe': [], '_angles':
> [], '_atoms': [< Atom 1: name 'C1' of type 'CH1' of resname '2ACG',
> resid 0 and segid 'seg_0_A001'>, < Atom 2: name 'O5' of type 'OA'
> of resname '2ACG', resid 0 and segid 'seg_0_A001'>, < Atom 3: name
> 'C5' of type 'CH1' of resname '2ACG', resid 0 and segid
> 'seg_0_A001'>, < Atom 4: name 'C4' of type 'CH1' of resname
> '2ACG', resid 0 and segid 'seg_0_A001'>, < Atom 5: name 'O4' of
> type 'OA' of resname '2ACG', resid 0 and segid 'seg_0_A001'>, <
> Atom 6: name 'C2' of type 'CH1' of resname '2ACG', resid 0 and segid
> 'seg_0_A001'>, < Atom 7: name 'O2' of type 'OE' of resname '2ACG',
> resid 0 and segid 'seg_0_A001'>, < Atom 8: name 'C7' of type 'C'
> of resname '2ACG', resid 0 and segid 'seg_0_A001'>, < Atom 9: name
> 'O7' of type 'O' of resname '2ACG', resid 0 and segid 'seg_0_A001'>,
> < Atom 10: name 'C8' of type 'CH3' of resname '2ACG', resid 0 and
> segid 'seg_0_A001'>, < Atom 11: name 'C3' of type 'CH1' of resname
> '2ACG', resid 0 and segid 'seg_0_A001'>, < Atom 12: name 'O3' of
> type 'OA' of resname '2ACG', resid 0 and segid 'seg_0_A001'>, <
> Atom 13: name 'H3' of type 'H' of resname '2ACG', resid 0 and segid
> 'seg_0_A001'>, < Atom 14: name 'C6' of type 'CH2' of resname
> '2ACG', resid 0 and segid 'seg_0_A001'>, < Atom 15: name 'O6' of
> type 'OA' of resname '2ACG', resid 0 and segid 'seg_0_A001'>, <
> Atom 16: name 'H6' of type 'H' of resname '2ACG', resid 0 and segid
> 'seg_0_A001'>, < Atom 17: name 'C1' of type 'CH1' of resname
> 'GCD', resid 1 and segid 'seg_0_A001'>, < Atom 18: name 'O5' of
> type 'OA' of resname 'GCD', resid 1 and segid 'seg_0_A001'>, <
> Atom 19: name 'C5' of type 'CH1' of resname 'GCD', resid 1 and segid
> 'seg_0_A001'>, < Atom 20: name 'C4' of type 'CH1' of resname
> 'GCD', resid 1 and segid 'seg_0_A001'>, < Atom 21: n(...)
>
> Does anyone know about any alternative?
>
> Thanks a lot for your help in advance.
>
> Best wishes,
>
> Rebeca
>
> Dr. Rebeca Garcia
> Santiago de Compostela University
> Spain
>
> ------------------------------
>
> Message: 2
> Date: Thu, 22 Jan 2015 19:28:24 +0800 (CST)
> From: xiao <helitrope at 126.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] QM/MM excited state optimization
> Message-ID: <36bf1892.2dcd6.14b11667ce9.Coremail.helitrope at 126.com>
> Content-Type: text/plain; charset=GBK
>
> Dear Gerrit,
>
>
> Thank you very much for your reply!
>
>
> I also use ORCA :). Do you mean that the geometry optimization is
> performed in ORCA but not in Gromacs, and in the other cases, the
> optimization is performed in Gromacs?
>
>
> Best regards
>
>
> Fugui
>
>
>
>
>
>
>
>
> At 2015-01-21 22:08:20, "Gerrit Groenhof" <ggroenh at gwdg.de> wrote:
> >Hi,
> >
> >Unless you use ORca, optimization can only be carried out with Gromacs's
> own optimization routines (steep, cg, or l-BFGS).
> >
> >The most critical aspect of your plan will be an accurate description of
> the correct electronic state.
> >
> >Best,
> >
> >Gerrit
> >
> >Dear Gromacs users,
> >
> >
> >I am interested in doing an geometrical optimization of an excited state
> of Tryptophan (an amino acid) in a protein. The method is a combination of
> Gromacs and Gaussian09. However, i found some information like that in the
> official website of Gromacs:?Optimization !!!! not working properly, I will
> fix this soon !!!!! ?http://wwwuser.gwdg.de/~ggroenh/qmmm.html?
> >
> >
> >I would like to know whether it is possible now to do optimization by
> QM/MM now in Gromacs?
> >
> >
> >Best regards
> >
> >
> >Fugui
> >
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >* For (un)subscribe requests visit
> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
> ------------------------------
>
> Message: 3
> Date: Thu, 22 Jan 2015 13:29:35 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] recovering topology from tpr
> Message-ID:
> <
> CAMNuMAS27ZtNzLepTphHwi0Fevb_vobgOeV9cE_h0J-NJGCtcw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Jan 22, 2015 at 12:11 PM, Rebeca Garc?a Fandi?o <
> regafan at hotmail.com
> > wrote:
>
> > Dear Gromacs users,
> > Is it posible to recover the topology files (itp or top) from a binary
> tpr
> > file?
> >
>
> I'm not aware of one, and even if it existed it could only reproduce a
> minimal version of the input, because grompp removes a lot of duplicated or
> unused things. Back up your files!
>
> Mark
>
>
> >
> > I have tried using this script:
> >
> >
> >
> https://pythonhosted.org/MDAnalysis/_modules/MDAnalysis/topology/TPRParser.html
> >
> > However, the itp file seems a single line like this:
> >
> > {'_bonds':
> > [(0, 3), (0, 7), (0, 11), (0, 13), (0, 74), (0, 80), (1, 4), (1, 6),
> > (1, 10), (1, 14), (1, 75), (2, 5), (2, 11), (2, 15), (2, 16), (2, 76),
> > (3, 6), (3, 12), (3, 14), (3, 17), (3, 21), (4, 5), (4, 11), (4, 13),
> > (4, 18), (4, 22), (4, 24), (5, 8), (5, 9), (5, 12), (5, 75), (6, 11),
> > (6, 76), (7, 10), (10, 13), (10, 16), (10, 76), (16, 19), (16, 23), (16,
> > 25), (16, 27), (17, 20), (17, 22), (17, 24), (17, 28), (18, 21), (18,
> > 25), (18, 29), (18, 30), (19, 22), (19, 26), (19, 28), (19, 31), (19,
> > 35), (20, 21), (20, 25), (20, 27), (20, 32), (20, 36), (20, 38), (21,
> > 26), (22, 25), (23, 24), (24, 27), (24, 30), (30, 33), (30, 37), (30,
> > 39), (30, 41), (31, 34), (31, 36), (31, 38), (31, 42), (32, 35), (32,
> > 39), (32, 43), (32, 44), (33, 36), (33, 40), (33, 42), (33, 45), (33,
> > 49), (34, 35), (34, 39), (34, 41), (34, 46), (34, 50), (34, 52), (35,
> > 40), (36, 39), (37, 38), (38, 41), (38, 44), (44, 47), (44, 51), (44,
> > 53), (44, 55), (45, 48), (45, 50), (45, 52), (45, 56), (46, 49), (46,
> > 53), (46, 57), (46, 58), (47, 50), (47, 54), (47, 56), (47, 59), (47,
> > 63), (48, 49), (48, 53), (48, 55), (48, 60), (48, 64), (48, 66), (49,
> > 54), (50, 53), (51, 52), (52, 55), (52, 58), (58, 61), (58, 65), (58,
> > 67), (58, 69), (59, 62), (59, 64), (59, 66), (59, 70), (60, 63), (60,
> > 67), (60, 71), (60, 72), (61, 64), (61, 68), (61, 70), (61, 73), (61,
> > 77), (62, 63), (62, 67), (62, 69), (62, 74), (62, 78), (62, 80), (63,
> > 68), (64, 67), (65, 66), (66, 69), (66, 72), (72, 75), (72, 79), (72,
> > 81), (72, 83), (73, 76), (73, 78), (73, 80), (73, 84), (74, 77), (74,
> > 81), (74, 85), (75, 78), (75, 82), (75, 84), (76, 77), (76, 81), (76,
> > 83), (77, 82), (78, 81), (79, 80), (80, 83)], '_dihe': [], '_angles':
> > [], '_atoms': [< Atom 1: name 'C1' of type 'CH1' of resname '2ACG',
> > resid 0 and segid 'seg_0_A001'>, < Atom 2: name 'O5' of type 'OA'
> > of resname '2ACG', resid 0 and segid 'seg_0_A001'>, < Atom 3: name
> > 'C5' of type 'CH1' of resname '2ACG', resid 0 and segid
> > 'seg_0_A001'>, < Atom 4: name 'C4' of type 'CH1' of resname
> > '2ACG', resid 0 and segid 'seg_0_A001'>, < Atom 5: name 'O4' of
> > type 'OA' of resname '2ACG', resid 0 and segid 'seg_0_A001'>, <
> > Atom 6: name 'C2' of type 'CH1' of resname '2ACG', resid 0 and segid
> > 'seg_0_A001'>, < Atom 7: name 'O2' of type 'OE' of resname '2ACG',
> > resid 0 and segid 'seg_0_A001'>, < Atom 8: name 'C7' of type 'C'
> > of resname '2ACG', resid 0 and segid 'seg_0_A001'>, < Atom 9: name
> > 'O7' of type 'O' of resname '2ACG', resid 0 and segid 'seg_0_A001'>,
> > < Atom 10: name 'C8' of type 'CH3' of resname '2ACG', resid 0 and
> > segid 'seg_0_A001'>, < Atom 11: name 'C3' of type 'CH1' of resname
> > '2ACG', resid 0 and segid 'seg_0_A001'>, < Atom 12: name 'O3' of
> > type 'OA' of resname '2ACG', resid 0 and segid 'seg_0_A001'>, <
> > Atom 13: name 'H3' of type 'H' of resname '2ACG', resid 0 and segid
> > 'seg_0_A001'>, < Atom 14: name 'C6' of type 'CH2' of resname
> > '2ACG', resid 0 and segid 'seg_0_A001'>, < Atom 15: name 'O6' of
> > type 'OA' of resname '2ACG', resid 0 and segid 'seg_0_A001'>, <
> > Atom 16: name 'H6' of type 'H' of resname '2ACG', resid 0 and segid
> > 'seg_0_A001'>, < Atom 17: name 'C1' of type 'CH1' of resname
> > 'GCD', resid 1 and segid 'seg_0_A001'>, < Atom 18: name 'O5' of
> > type 'OA' of resname 'GCD', resid 1 and segid 'seg_0_A001'>, <
> > Atom 19: name 'C5' of type 'CH1' of resname 'GCD', resid 1 and segid
> > 'seg_0_A001'>, < Atom 20: name 'C4' of type 'CH1' of resname
> > 'GCD', resid 1 and segid 'seg_0_A001'>, < Atom 21: n(...)
> >
> > Does anyone know about any alternative?
> >
> > Thanks a lot for your help in advance.
> >
> > Best wishes,
> >
> > Rebeca
> >
> > Dr. Rebeca Garcia
> > Santiago de Compostela University
> > Spain
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 22 Jan 2015 05:34:08 -0800
> From: marzieh dehghan <dehghanmarzieh at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] how can we modify *.rtp file?
> Message-ID:
> <CA+6Z3Gneva-zxfiTYZqE33B45bD9NPD2Z6sneg3+=
> 3pY_DpqXw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi every body
>
> we would like to simulate a covalent modification on a protein by gromacs.
> Based on gromacs tutorial, modification is introduced as a new amino acids,
> so we changed *.rtp file. As a trick, we used parameters in output file
> (*.top) of topolbuild and prodrug server to modify the *.rtp file. We
> filled Atom, atom type, atom charge and charge group fields in the amino
> acids.rtp, but we don't know how to determine gb_xx and ga_aa, etc?
>
> thanks a lot
>
>
> --
>
>
>
>
> *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
> Biophysics (IBB)University of Tehran, Tehran- Iran.*
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 22 Jan 2015 08:44:42 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] how can we modify *.rtp file?
> Message-ID: <54C0FECA.40503 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 1/22/15 8:34 AM, marzieh dehghan wrote:
> > Hi every body
> >
> > we would like to simulate a covalent modification on a protein by
> gromacs.
> > Based on gromacs tutorial, modification is introduced as a new amino
> acids,
> > so we changed *.rtp file. As a trick, we used parameters in output file
> > (*.top) of topolbuild and prodrug server to modify the *.rtp file. We
> > filled Atom, atom type, atom charge and charge group fields in the amino
> > acids.rtp, but we don't know how to determine gb_xx and ga_aa, etc?
> >
>
> These are essentially just preprocessor directives that label which
> interaction
> should be used. Look in ffbonded.itp and you will see how each parameter
> is
> mapped to each sequence of atom types.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 22 Jan 2015 19:29:45 +0530
> From: Sahithya S Iyer <sah2714 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] constant pH simulations in GROMACS 4.5
> Message-ID:
> <
> CACPrdiQc9ufNboGcyM0n0xbVY7pFNDd4DZ0fVZN1-geVtCbycQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi users
> Have standard methods been developed in
> Gromacs
> 4.5 version to perform constant pH simulations ?
> --
> Sahithya
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
> End of gromacs.org_gmx-users Digest, Vol 129, Issue 75
> ******************************************************
>
--
*Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
Biophysics (IBB)University of Tehran, Tehran- Iran.*
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