Thanks Daniel. The rst command worked.
Suchetana Gupta
IIT Madras
On Thu, Aug 31, 2017 at 12:30 AM, <amber-request.ambermd.org> wrote:
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: Closest velocities (Daniel Roe)
> 2. Re: Distance Restraint using COM for Umbrella Sampling
> (Daniel Roe)
> 3. Re: Calculation the Area per lipids using cpptraj (Daniel Roe)
> 4. Re: Clarification about Gnp settings in MM/PBSA (Guqin Shi)
> 5. Re: Query regarding water-water interaction potential in GIST
> output (Rakesh Srivastava)
> 6. Re: Calculation the Area per lipids using cpptraj
> (James Starlight)
> 7. TIP3PBOX for membrane system (James Starlight)
> 8. Re: (kein Betreff) (Traeg, Johannes)
> 9. Re: TIP3PBOX for membrane system (Bill Ross)
> 10. Re: TIP3PBOX for membrane system (James Starlight)
> 11. Re: TIP3PBOX for membrane system (Bill Ross)
> 12. Re: TIP3PBOX for membrane system (James Starlight)
> 13. Re: TIP3PBOX for membrane system (Bill Ross)
> 14. Re: TIP3PBOX for membrane system (James Starlight)
> 15. Re: (kein Betreff) (Junmei Wang)
> 16. Re: Deprotonation of Tyr (pancham lal Gupta)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 29 Aug 2017 15:26:03 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Closest velocities
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOZ925Bu2HEPQM3OFK4OGNFM7pqAcYQy2qJwSmuyfUQHiA.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> You will have to use a format that supports both coordinates and
> velocities (like NetCDF or Amber restart). If you need the Amber ASCII
> trajectory format I will have to add a keyword so that the velocities
> will be written in place of the coordinates (making it a "MDVEL"
> file). Let me know if you would like this functionality.
>
> -Dan
>
> On Tue, Aug 29, 2017 at 3:31 AM, P?r H?kansson <Nils.Hakansson.oulu.fi>
> wrote:
> > Thanks for the suggestion, however I still have problems
> > (I am trying to educate my self on cpptraj, I mainly used some basic
> ptraj commands before):
> > I want to read mdcrd and mdvel files, find the closest solvents and
> printout the stripped mdcrd and mdvel files
> > (or a combined file).
> >
> > I tired the following (testing with two frames):
> > parm Acet_meoh.prmtop
> > trajin mdcrd mdvel 1 2 1
> > trajout mdcrd
> > solvent byres :MOH
> > closest 8 :MOL.C1,C2 oxygen closestout closest_meohtest.dat outprefix
> closesttest
> > go
> >
> > There is no message that velocity files are read and no velocity
> information in the output so above does not work,
> > hence my question is if it is possible to read both mdcrd and mdvel
> files (or transform them to a NetCDF format)?
> >
> > Kind regards,
> > P?r
> >
> > ________________________________________
> > Fr?n: Daniel Roe <daniel.r.roe.gmail.com>
> > Skickat: den 24 augusti 2017 23:00
> > Till: AMBER Mailing List
> > ?mne: Re: [AMBER] Closest velocities
> >
> > If the velocities are present in the input trajectory they should be
> > present in any output trajectory when 'closest' is used. So you can
> > just use 'trajout' to write an output trajectory.
> >
> > -Dan
> >
> > On Thu, Aug 24, 2017 at 3:20 PM, P?r H?kansson <Nils.Hakansson.oulu.fi>
> wrote:
> >> Dear Amber list,
> >>
> >>
> >> Using AmberToos16, I have extracted the eight closest solvent molecules
> to my s?olute "MOL"
> >>
> >> with the following line in cpptraj script:
> >>
> >>
> >>>closest 8 :MOL.C1,C2 oxygen closestout closest_meoh.dat outprefix
> closest
> >>
> >>
> >> providing a striped set of coordinates of MOL+8solvents.
> >>
> >>
> >> I have solvent index for each timestep in "closest_meoh.dat", and I
> could
> >>
> >> write my own program/script. However,
> >>
> >> my question is if there is any route to use cpptraj (or other available
> tools)
> >>
> >> to extract the corresponding velocities?
> >>
> >>
> >> Kind regards,
> >>
> >> P?r
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 29 Aug 2017 15:29:06 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Distance Restraint using COM for Umbrella
> Sampling
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOZ8QN=DFSkuSn_gzF_0XXKov+S1=fE70p3NpJnvt52umQ.
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> The 'rst' command in cpptraj can convert regular Amber mask
> expressions to Amber group format. For example:
>
> > rst :1 :12 r1 2 r2 3.5 r3 3.5 r4 5 rk2 5 rk3 5
> Mask [:1] corresponds to 13 atoms.
> Mask [:12] corresponds to 22 atoms.
> &rst iat=-1,-1,0
> r1=2.000000, r2=3.500000, r3=3.500000, r4=5.000000, rk2=5.000000,
> rk3=5.000000,
> IGR1(1)=1,IGR1(2)=2,IGR1(3)=3,IGR1(4)=4,IGR1(5)=5,IGR1(6)=6,
> IGR1(7)=7,IGR1(8)=8,IGR1(9)=9,IGR1(10)=10,IGR1(11)=11,IGR1(
> 12)=12,IGR1(13)=13,
> IGR2(1)=196,IGR2(2)=197,IGR2(3)=198,IGR2(4)=199,IGR2(5)=
> 200,IGR2(6)=201,IGR2(7)=202,IGR2(8)=203,IGR2(9)=204,IGR2(
> 10)=205,IGR2(11)=206,IGR2(12)=207,IGR2(13)=208,IGR2(14)=209,
> IGR2(15)=210,IGR2(16)=211,IGR2(17)=212,IGR2(18)=213,
> IGR2(19)=214,IGR2(20)=215,IGR2(21)=216,IGR2(22)=217,
> nstep1=0, nstep2=0,
> &end
>
> See the manual for full details.
>
> -Dan
>
>
> On Tue, Aug 29, 2017 at 8:56 AM, Suchetana Gupta <tutulg.gmail.com> wrote:
> > Dear Amber users
> > I want to perform umbrella sampling on my protein of interest. What will
> be
> > the format for specifying the COM of certain residues (say I want to
> apply
> > restraint on residues x to y)? I realised that I can manually write all
> the
> > atom numbers using iat and igr, but is there any existing format to do it
> > automatically? Also, is it true that the iat can read only upto 200 atoms
> > at a time?
> > Thanks in advance
> > Suchetana Gupta
> > IIT Madras
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 29 Aug 2017 15:35:33 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] Calculation the Area per lipids using cpptraj
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOZdYCTknp6wC94UG74N2jw0yj9NufAi1_PfD4yVjm-Pig.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> nmols is the total number of lipid molecules. In this case you have
> 120 lipids so 'nmols 120'. However, if you're giving cpptraj a mask
> then you don't need to specify nmols since it will be calculated.
>
> -Dan
>
> On Wed, Aug 23, 2017 at 9:33 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> > Thanks you!
> >
> > Because of the splitting of the lipids on three residues in Lipid14,
> > should I use it for the following options?
> >
> > # calculation of apl for popc bilayer composed of 120 lipids
> > areapermol OL_area :OL,PA,PC nlayers 2 nmols 60 out apm.dat
> >
> > nmols should be provided for 1 leaflet only?
> >
> > Thank you!
> >
> > James
> >
> > 2017-08-21 15:28 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> >> Hi,
> >>
> >> I recommend just using the 'areapermol' action from cpptraj which
> >> performs the same procedure in a simpler fashion.
> >>
> >> -Dan
> >>
> >>
> >> On Mon, Aug 21, 2017 at 4:19 AM, James Starlight <
> jmsstarlight.gmail.com> wrote:
> >>> Dear all,
> >>>
> >>> there is some problem in the script for calculation of area per lipids
> >>> following the lipid tutorial.
> >>>
> >>>
> >>> If I have in the cpptraj script the following string:
> >>>
> >>> vector test * box out vector.dat
> >>>
> >>> I have obtained the error from cpptraj:
> >>>
> >>> VECTOR: Type Box, output to vector.dat
> >>> Error: [vector] Not all arguments handled: [ * ]
> >>> 1 errors encountered reading input.
> >>> TIME: Total execution time: 0.2326 seconds.
> >>>
> >>> If I have the same string without atom selection:
> >>> vector test box out vector.dat
> >>>
> >>> there is no error.
> >>>
> >>> How the syntax should be corrected?
> >>>
> >>> Thanks!
> >>>
> >>> James
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe
> >> Laboratory of Computational Biology
> >> National Institutes of Health, NHLBI
> >> 5635 Fishers Ln, Rm T900
> >> Rockville MD, 20852
> >> https://www.lobos.nih.gov/lcb
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 29 Aug 2017 16:00:47 -0400
> From: Guqin Shi <shi.293.osu.edu>
> Subject: Re: [AMBER] Clarification about Gnp settings in MM/PBSA
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CACUf8Hdq=dC0FrkC57n4R4WnbFSMw6Q0pPNFKDDJ5OUPx6Agew.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Also, I have a followed-up question. No matter what cavity_surften and
> cavity_offset settings I used in MM/PBSA, as long as other settings are the
> same, is the SASA term calculated by same program PBSA? Since I chose inp=1
> which is a linear model, theoretically the average Enp could be transformed
> directly without recalculating MM/PBSA if I only want to get different
> Enp...Is that correct?
>
> Thanks!
> Guqin
>
> On Tue, Aug 29, 2017 at 2:35 PM, Guqin Shi <shi.293.osu.edu> wrote:
>
> > Dear all,
> >
> > I have a simple question that I hope somebody could clarify for me. It's
> > about the Gnp settings in MM/PBSA.
> >
> > &pb and &gb has different namelist variables. I am using inp=1 option
> > which calculates Gnp linearly to SASA (gamma*SASA+b). There are different
> > sets of gamma and b.
> >
> > In &pb namelist, I used cavity_surften (gamma) and cavity_offset (b) to
> > change the settings for Gnp.
> > (In &gb namelist, surften (gamma) and surfoff (b) are used.)
> >
> > I usually ask program to print out all temporary files for me during
> > MM/PBSA. There is one file _MMPBSA_info which contains all input
> > parameters. I checked this file and noticed that both surften, surfoff,
> > cavity_surften, and cavity_offset are listed. surften and surfoff are
> their
> > default values (according to Amber manuals under &gb section). I am a
> > little bit confused. So here _MMPBSA_info file just listed all parameters
> > but eventually if I specified &pb, then the program will only use
> > cavity_surften and cavity_offset for Gnp calculation, right? I want to
> make
> > sure I pass the correct parameters to the program...
> >
> > Thank you a lot!
> > -Guqin
> >
> > --
> > Guqin SHI
> > PhD Candidate in Medicinal Chemistry and Pharmacognosy
> > College of Pharmacy
> > The Ohio State University
> > Columbus, OH, 43210
> >
> >
>
>
> --
> Guqin SHI
> PhD Candidate in Medicinal Chemistry and Pharmacognosy
> College of Pharmacy
> The Ohio State University
> Columbus, OH, 43210
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 30 Aug 2017 09:52:07 +0530
> From: Rakesh Srivastava <allahabad.21.gmail.com>
> Subject: Re: [AMBER] Query regarding water-water interaction potential
> in GIST output
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAC6hn06r6z_6=s9Ff6fdWQyb_e-Aq2RUeUEMG-UGcDfQcAiVvg.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thanks Steven..
>
> Rakesh Srivastava
> Research Fellow
> School of Computational & Integrative Sciences
> Jawaharlal Nehru University, New Delhi-110067
> India
>
>
> On Tue, Aug 29, 2017 at 7:33 PM, Steven Ramsey <vpsramsey.gmail.com>
> wrote:
>
> > Hello Rakesh,
> >
> > The water-water energies reported in GIST are indeed corrected to avoid
> > double counting. The 'unreferenced' refers to the energies being
> determined
> > directly from the sampled frames and not compared to some reference
> > quantity (such as bulk).
> >
> > Hope this helps,
> >
> > --Steve
> >
> > On Tue, Aug 29, 2017 at 7:56 AM, Rakesh Srivastava <
> allahabad.21.gmail.com
> > >
> > wrote:
> >
> > > Hello everyone,
> > >
> > > Please let me know that, the unreferenced water-water interaction
> > potential
> > > we get in GIST output, has been corrected for double counting or not ?
> > >
> > > Thanks in advance.
> > >
> > > Rakesh Srivastava
> > > Research Fellow
> > > School of Computational & Integrative Sciences
> > > Jawaharlal Nehru University, New Delhi-110067
> > > India
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 30 Aug 2017 10:00:03 +0200
> From: James Starlight <jmsstarlight.gmail.com>
> Subject: Re: [AMBER] Calculation the Area per lipids using cpptraj
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAALQopxSXCYwZ_vH3VzjYf3WuSgY+KbwMDW+
> oV3ZaE09Okv2CQ.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> and how to define mask properly for the lipid e.g POPC?
> if I use :OL it works good
> but
> :OL,PA,PC calculate wrong area
>
> James
>
> 2017-08-29 21:35 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> > nmols is the total number of lipid molecules. In this case you have
> > 120 lipids so 'nmols 120'. However, if you're giving cpptraj a mask
> > then you don't need to specify nmols since it will be calculated.
> >
> > -Dan
> >
> > On Wed, Aug 23, 2017 at 9:33 AM, James Starlight <jmsstarlight.gmail.com>
> wrote:
> >> Thanks you!
> >>
> >> Because of the splitting of the lipids on three residues in Lipid14,
> >> should I use it for the following options?
> >>
> >> # calculation of apl for popc bilayer composed of 120 lipids
> >> areapermol OL_area :OL,PA,PC nlayers 2 nmols 60 out apm.dat
> >>
> >> nmols should be provided for 1 leaflet only?
> >>
> >> Thank you!
> >>
> >> James
> >>
> >> 2017-08-21 15:28 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> >>> Hi,
> >>>
> >>> I recommend just using the 'areapermol' action from cpptraj which
> >>> performs the same procedure in a simpler fashion.
> >>>
> >>> -Dan
> >>>
> >>>
> >>> On Mon, Aug 21, 2017 at 4:19 AM, James Starlight <
> jmsstarlight.gmail.com> wrote:
> >>>> Dear all,
> >>>>
> >>>> there is some problem in the script for calculation of area per lipids
> >>>> following the lipid tutorial.
> >>>>
> >>>>
> >>>> If I have in the cpptraj script the following string:
> >>>>
> >>>> vector test * box out vector.dat
> >>>>
> >>>> I have obtained the error from cpptraj:
> >>>>
> >>>> VECTOR: Type Box, output to vector.dat
> >>>> Error: [vector] Not all arguments handled: [ * ]
> >>>> 1 errors encountered reading input.
> >>>> TIME: Total execution time: 0.2326 seconds.
> >>>>
> >>>> If I have the same string without atom selection:
> >>>> vector test box out vector.dat
> >>>>
> >>>> there is no error.
> >>>>
> >>>> How the syntax should be corrected?
> >>>>
> >>>> Thanks!
> >>>>
> >>>> James
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>>
> >>> --
> >>> -------------------------
> >>> Daniel R. Roe
> >>> Laboratory of Computational Biology
> >>> National Institutes of Health, NHLBI
> >>> 5635 Fishers Ln, Rm T900
> >>> Rockville MD, 20852
> >>> https://www.lobos.nih.gov/lcb
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe
> > Laboratory of Computational Biology
> > National Institutes of Health, NHLBI
> > 5635 Fishers Ln, Rm T900
> > Rockville MD, 20852
> > https://www.lobos.nih.gov/lcb
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 30 Aug 2017 11:25:00 +0200
> From: James Starlight <jmsstarlight.gmail.com>
> Subject: [AMBER] TIP3PBOX for membrane system
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAALQopy6oOYWoWGHaQJD9tNHHQy6-1GrgkeV4QZjbfEH1JNAug.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear amber users!
>
> I am using tleap to generate water box for the GPCR protein embedded
> within the 120 lipids.
>
> solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
>
> My question: what the params for solvatebox may be desirable to
> generate a proper number of water along Z dimensions of the membrane?
>
> Thanks!
>
> James
>
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 30 Aug 2017 11:28:48 +0200
> From: "Traeg, Johannes" <johannes.traeg.fau.de>
> Subject: Re: [AMBER] (kein Betreff)
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <2dea9ff6401e7914725e368250115124.fau.de>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Hello Junmei,
>
> i also tried with 5-ethyl-1H-1,2,3-triazole and got the correct dihedral
> parameters. However, for 4-ethyl-1H-1,2,3-triazole it does not work.
> The difference between both molecules is that in one case antechamber
> ascribes the dihedral c3-c3-cc-cd (5-ethyl) and in the other case
> antechamber ascribes the dihedral c3-c3-cd-cc (4-ethyl). The latter
> dihedral defaults to the dihedral X-c3-cd-X, while the first one does
> not default to X-c3-cc-X, but takes the value of the explicit dihedral
> c3-c3-cc-cd. However, due to the equivalence of cd and cc, one would
> expect to get the same values for both dihedrals.
>
> How would you proceed to solve this problem?
>
> Best regards
>
> Johannes
>
>
>
>
> Am 2017-08-29 16:02, schrieb Junmei Wang:
> > Also, cd-cc-c3-c3 was introduced only in gaff2 (0.157, 0.0, 3). In
> > gaff,
> > the force constant of cd-cc-c3-c3 is 0.0 (X-cc-c3-X 6 0.0 3.0).
> >
> > Best
> >
> > Junmei
> >
> > On Tue, Aug 29, 2017 at 9:54 AM, Junmei Wang <junmwang.gmail.com>
> > wrote:
> >
> >> Hello, Johannes,
> >>
> >> When you ran parmchk2, did you specify to use gaff2 with "-s 2"? The
> >> default FF to use is gaff, not gaff2.
> >>
> >> I constructed two triazole molecules (ethyl triazole and
> >> 5-ethyl-1H-1,2,3-triazole) and assigned both gaff and gaff2 atom
> >> types. I
> >> didn't find a problem with the four frcmod files produced by parmchk2.
> >>
> >> Please also use "-at gaff2" when you run antechamber to assign gaff2
> >> atom
> >> types.
> >>
> >> Please let me know if you have more questions.
> >>
> >> Best
> >>
> >> Junmei
> >>
> >> On Tue, Aug 22, 2017 at 4:47 AM, Traeg, Johannes
> >> <johannes.traeg.fau.de>
> >> wrote:
> >>
> >>> Hi AMBER users,
> >>>
> >>> I'm having trouble with a GAFF2 force field that I generated with
> >>> ANTECHAMBER/LEAP. My molecule contains a triazole unit with an ethyl
> >>> group connected to one of the carbon atoms of triazole. ANTECHAMBER
> >>> correctly recognizes the atom types and, hence, my molecule contains
> >>> the
> >>> dihedral CC-CD-C3-C3 (CC and CD are identical in GAFF/GAFF2). The
> >>> .prmtop file lists the following parameters for this dihedral:
> >>>
> >>> force constant = 0.0
> >>> phase = 0.0
> >>> periodicity = 3
> >>>
> >>> However, the GAFF2.dat file (Amber16) lists the following parameters
> >>> for
> >>> the dihedral CD-CC-C3-C3, which should be identical to CC-CD-C3-C3
> >>> (due
> >>> to the equivalence of CC and CD):
> >>>
> >>> force constant = 0.157
> >>> phase = 180.0
> >>> periodicity = 3
> >>>
> >>> Can anyone help me out with this problem?
> >>>
> >>> Thanks in advance and best regards,
> >>>
> >>> Johannes
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 9
> Date: Wed, 30 Aug 2017 02:30:58 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] TIP3PBOX for membrane system
> To: amber.ambermd.org
> Message-ID: <65e58884-b35e-bc49-e574-2bb79eec6143.cgl.ucsf.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Experiment - 'edit mymol' in xleap will make it go fast.
>
> Bill
>
>
> On 8/30/17 2:25 AM, James Starlight wrote:
> > Dear amber users!
> >
> > I am using tleap to generate water box for the GPCR protein embedded
> > within the 120 lipids.
> >
> > solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
> >
> > My question: what the params for solvatebox may be desirable to
> > generate a proper number of water along Z dimensions of the membrane?
> >
> > Thanks!
> >
> > James
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Wed, 30 Aug 2017 11:39:21 +0200
> From: James Starlight <jmsstarlight.gmail.com>
> Subject: Re: [AMBER] TIP3PBOX for membrane system
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAALQopxWW0T77N5vEeHUO5LzsRHMj9yrj_=p-zKBbW_t+Vrs8A.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> I need it to make in tleap because it is a part of some script for
> automatic GPCR preparation. After tleap I post-process the system with
> some python script which cut the water licked into the membrane during
> to solvation - it is not a problem.
> Thus, initially I need to add correct number of waters above the
> lipid leaflets of the system (along Z) with receptor and lipids only.
> I don't understand what is 1.5 number in
> solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
>
> 2017-08-30 11:30 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> > Experiment - 'edit mymol' in xleap will make it go fast.
> >
> > Bill
> >
> >
> > On 8/30/17 2:25 AM, James Starlight wrote:
> >> Dear amber users!
> >>
> >> I am using tleap to generate water box for the GPCR protein embedded
> >> within the 120 lipids.
> >>
> >> solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
> >>
> >> My question: what the params for solvatebox may be desirable to
> >> generate a proper number of water along Z dimensions of the membrane?
> >>
> >> Thanks!
> >>
> >> James
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 11
> Date: Wed, 30 Aug 2017 02:41:50 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] TIP3PBOX for membrane system
> To: amber.ambermd.org
> Message-ID: <08befa4c-e6a1-9834-5af6-28eced39b645.cgl.ucsf.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Try 'help solvatebox' - I think it's a factor for packing. Packmol is
> another prog people use for building boxes, may be more flexible.
>
>
> On 8/30/17 2:39 AM, James Starlight wrote:
> > I need it to make in tleap because it is a part of some script for
> > automatic GPCR preparation. After tleap I post-process the system with
> > some python script which cut the water licked into the membrane during
> > to solvation - it is not a problem.
> > Thus, initially I need to add correct number of waters above the
> > lipid leaflets of the system (along Z) with receptor and lipids only.
> > I don't understand what is 1.5 number in
> > solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
> >
> > 2017-08-30 11:30 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> >> Experiment - 'edit mymol' in xleap will make it go fast.
> >>
> >> Bill
> >>
> >>
> >> On 8/30/17 2:25 AM, James Starlight wrote:
> >>> Dear amber users!
> >>>
> >>> I am using tleap to generate water box for the GPCR protein embedded
> >>> within the 120 lipids.
> >>>
> >>> solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
> >>>
> >>> My question: what the params for solvatebox may be desirable to
> >>> generate a proper number of water along Z dimensions of the membrane?
> >>>
> >>> Thanks!
> >>>
> >>> James
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 12
> Date: Wed, 30 Aug 2017 11:42:57 +0200
> From: James Starlight <jmsstarlight.gmail.com>
> Subject: Re: [AMBER] TIP3PBOX for membrane system
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAALQopyRkQpz+TUD3tvyJh5brx7DGd5H6FmRhJ68deW
> exObD0Q.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> OK, thank you!
>
> 2017-08-30 11:41 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> > Try 'help solvatebox' - I think it's a factor for packing. Packmol is
> > another prog people use for building boxes, may be more flexible.
> >
> >
> > On 8/30/17 2:39 AM, James Starlight wrote:
> >> I need it to make in tleap because it is a part of some script for
> >> automatic GPCR preparation. After tleap I post-process the system with
> >> some python script which cut the water licked into the membrane during
> >> to solvation - it is not a problem.
> >> Thus, initially I need to add correct number of waters above the
> >> lipid leaflets of the system (along Z) with receptor and lipids only.
> >> I don't understand what is 1.5 number in
> >> solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
> >>
> >> 2017-08-30 11:30 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> >>> Experiment - 'edit mymol' in xleap will make it go fast.
> >>>
> >>> Bill
> >>>
> >>>
> >>> On 8/30/17 2:25 AM, James Starlight wrote:
> >>>> Dear amber users!
> >>>>
> >>>> I am using tleap to generate water box for the GPCR protein embedded
> >>>> within the 120 lipids.
> >>>>
> >>>> solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
> >>>>
> >>>> My question: what the params for solvatebox may be desirable to
> >>>> generate a proper number of water along Z dimensions of the membrane?
> >>>>
> >>>> Thanks!
> >>>>
> >>>> James
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 13
> Date: Wed, 30 Aug 2017 02:43:17 -0700
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] TIP3PBOX for membrane system
> To: amber.ambermd.org
> Message-ID: <d8388c64-3b52-3066-6bae-282e94848252.cgl.ucsf.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Also, you can experiment interactively in xleap til you figure out what
> works, then use it in tleap for production. You just want to see water
> placement quickly before trying another permutation.
>
>
> On 8/30/17 2:39 AM, James Starlight wrote:
> > I need it to make in tleap because it is a part of some script for
> > automatic GPCR preparation. After tleap I post-process the system with
> > some python script which cut the water licked into the membrane during
> > to solvation - it is not a problem.
> > Thus, initially I need to add correct number of waters above the
> > lipid leaflets of the system (along Z) with receptor and lipids only.
> > I don't understand what is 1.5 number in
> > solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
> >
> > 2017-08-30 11:30 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> >> Experiment - 'edit mymol' in xleap will make it go fast.
> >>
> >> Bill
> >>
> >>
> >> On 8/30/17 2:25 AM, James Starlight wrote:
> >>> Dear amber users!
> >>>
> >>> I am using tleap to generate water box for the GPCR protein embedded
> >>> within the 120 lipids.
> >>>
> >>> solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
> >>>
> >>> My question: what the params for solvatebox may be desirable to
> >>> generate a proper number of water along Z dimensions of the membrane?
> >>>
> >>> Thanks!
> >>>
> >>> James
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 14
> Date: Wed, 30 Aug 2017 11:54:33 +0200
> From: James Starlight <jmsstarlight.gmail.com>
> Subject: Re: [AMBER] TIP3PBOX for membrane system
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAALQopyu3L=esX2zXT2rT0NbVgY-S+1jdwgEaukmC_dLhFOFTg.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Yep, you are right.
> This term is related to packing of the water. The value > 2.0 produces
> large emptiness cavities between water layer and membrane which seems
> not good..
>
> 2017-08-30 11:43 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> > Also, you can experiment interactively in xleap til you figure out what
> > works, then use it in tleap for production. You just want to see water
> > placement quickly before trying another permutation.
> >
> >
> > On 8/30/17 2:39 AM, James Starlight wrote:
> >> I need it to make in tleap because it is a part of some script for
> >> automatic GPCR preparation. After tleap I post-process the system with
> >> some python script which cut the water licked into the membrane during
> >> to solvation - it is not a problem.
> >> Thus, initially I need to add correct number of waters above the
> >> lipid leaflets of the system (along Z) with receptor and lipids only.
> >> I don't understand what is 1.5 number in
> >> solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
> >>
> >> 2017-08-30 11:30 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> >>> Experiment - 'edit mymol' in xleap will make it go fast.
> >>>
> >>> Bill
> >>>
> >>>
> >>> On 8/30/17 2:25 AM, James Starlight wrote:
> >>>> Dear amber users!
> >>>>
> >>>> I am using tleap to generate water box for the GPCR protein embedded
> >>>> within the 120 lipids.
> >>>>
> >>>> solvatebox protein TIP3PBOX { 0.0 0.0 15 } 1.5
> >>>>
> >>>> My question: what the params for solvatebox may be desirable to
> >>>> generate a proper number of water along Z dimensions of the membrane?
> >>>>
> >>>> Thanks!
> >>>>
> >>>> James
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 15
> Date: Wed, 30 Aug 2017 11:27:44 -0400
> From: Junmei Wang <junmwang.gmail.com>
> Subject: Re: [AMBER] (kein Betreff)
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAE0aOoRXEBaAAsrxNiadX-Foev-NAcDHbOitevbK7KB301QWAw.mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> I see. Please add the torsional angle parameter of cc-cd-c3-c3 to gaff2.dat
> "cc-cd-c3-c3 1 0.157 180.0 3"
>
> I will check gaff2.dat and make sure all the equivalent parameters exist.
>
> Thanks a lot.
>
> Junmei
>
> On Wed, Aug 30, 2017 at 5:28 AM, Traeg, Johannes <johannes.traeg.fau.de>
> wrote:
>
> > Hello Junmei,
> >
> > i also tried with 5-ethyl-1H-1,2,3-triazole and got the correct dihedral
> > parameters. However, for 4-ethyl-1H-1,2,3-triazole it does not work.
> > The difference between both molecules is that in one case antechamber
> > ascribes the dihedral c3-c3-cc-cd (5-ethyl) and in the other case
> > antechamber ascribes the dihedral c3-c3-cd-cc (4-ethyl). The latter
> > dihedral defaults to the dihedral X-c3-cd-X, while the first one does
> > not default to X-c3-cc-X, but takes the value of the explicit dihedral
> > c3-c3-cc-cd. However, due to the equivalence of cd and cc, one would
> > expect to get the same values for both dihedrals.
> >
> > How would you proceed to solve this problem?
> >
> > Best regards
> >
> > Johannes
> >
> >
> >
> >
> > Am 2017-08-29 16:02, schrieb Junmei Wang:
> > > Also, cd-cc-c3-c3 was introduced only in gaff2 (0.157, 0.0, 3). In
> > > gaff,
> > > the force constant of cd-cc-c3-c3 is 0.0 (X-cc-c3-X 6 0.0 3.0).
> > >
> > > Best
> > >
> > > Junmei
> > >
> > > On Tue, Aug 29, 2017 at 9:54 AM, Junmei Wang <junmwang.gmail.com>
> > > wrote:
> > >
> > >> Hello, Johannes,
> > >>
> > >> When you ran parmchk2, did you specify to use gaff2 with "-s 2"? The
> > >> default FF to use is gaff, not gaff2.
> > >>
> > >> I constructed two triazole molecules (ethyl triazole and
> > >> 5-ethyl-1H-1,2,3-triazole) and assigned both gaff and gaff2 atom
> > >> types. I
> > >> didn't find a problem with the four frcmod files produced by parmchk2.
> > >>
> > >> Please also use "-at gaff2" when you run antechamber to assign gaff2
> > >> atom
> > >> types.
> > >>
> > >> Please let me know if you have more questions.
> > >>
> > >> Best
> > >>
> > >> Junmei
> > >>
> > >> On Tue, Aug 22, 2017 at 4:47 AM, Traeg, Johannes
> > >> <johannes.traeg.fau.de>
> > >> wrote:
> > >>
> > >>> Hi AMBER users,
> > >>>
> > >>> I'm having trouble with a GAFF2 force field that I generated with
> > >>> ANTECHAMBER/LEAP. My molecule contains a triazole unit with an ethyl
> > >>> group connected to one of the carbon atoms of triazole. ANTECHAMBER
> > >>> correctly recognizes the atom types and, hence, my molecule contains
> > >>> the
> > >>> dihedral CC-CD-C3-C3 (CC and CD are identical in GAFF/GAFF2). The
> > >>> .prmtop file lists the following parameters for this dihedral:
> > >>>
> > >>> force constant = 0.0
> > >>> phase = 0.0
> > >>> periodicity = 3
> > >>>
> > >>> However, the GAFF2.dat file (Amber16) lists the following parameters
> > >>> for
> > >>> the dihedral CD-CC-C3-C3, which should be identical to CC-CD-C3-C3
> > >>> (due
> > >>> to the equivalence of CC and CD):
> > >>>
> > >>> force constant = 0.157
> > >>> phase = 180.0
> > >>> periodicity = 3
> > >>>
> > >>> Can anyone help me out with this problem?
> > >>>
> > >>> Thanks in advance and best regards,
> > >>>
> > >>> Johannes
> > >>>
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 16
> Date: Wed, 30 Aug 2017 11:40:08 -0400
> From: pancham lal Gupta <panchamlalgupta.gmail.com>
> Subject: Re: [AMBER] Deprotonation of Tyr
> To: AMBER Mailing List <amber.ambermd.org>, soemya.kemi.dtu.dk
> Message-ID:
> <CAC9pAd86GHNKZczRQdLkrEAE+E5HizRBzco8MK3cSU9DfDsKQA.
> mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Sowmya,
>
> Sorry for late reply, both cc'ed email didn't arrive in Inbox.
>
>
> If you want to keep specific TYR and LYS in deprotonated or protonated
> state through out constant pH MD simulation then do not put them in
> titrating residue list. When you are creating cpin file by using
> cpinutil.py, do not mention those residue names.
>
> In CpHMD/pH-REMD protocol, titratable residues are parametrized with all
> possible protons. These protons retain their position through out CpHMD
> simulation. Suppose Tyr is in protonated state and during CpHMD, it was
> allowed to change into deprotonated state. Then zero charge will be
> assigned to titratable proton and charges on backbone and side-chain atoms
> will be updated according to deprotonated state of Tyr residue. (Read
> protonation State Models section in this paper -
> http://doi.wiley.com/10.1002/jcc.20139 )
>
> CpHMD/pH-REMD prmtop and trajectory files will have all titratable protons
> atomtypes and co-ordinates irrespective of protonation state. That's why,
> Tyr's titratable proton co-ordinates were there in pdb file. Protonation
> state information of residue will only be in cpout files. That's why, to
> analyze CpHMD/pH-REMD trajectories, cpout and trajectories files must be
> used together. One example is given here-
> http://ambermd.org/tutorials/advanced/tutorial18/section4.htm. In this
> example, a tcl script has been written by using cpout files which will
> delete all "ghost" protons while visualizing in vmd.
>
>
> Let me know if it clear some doubts,
>
>
> Pancham Lal
> PhD, Department of Chemistry
> University of Florida
>
>
> On Sun, Aug 20, 2017 at 9:45 AM, Sowmya Indrakumar <soemya.kemi.dtu.dk>
> wrote:
>
> > Dear All,
> >
> > I want to keep certain TYR in the deprotonated state and one LYS
> > protonated while performing constpH MD at pH=7.4 and IS= 0.1M
> >
> > I generated the initial cpin file and a new parameter file using the
> below
> > mentioned command:
> >
> > cpinutil.py -p model_sol.parm7 -igb 2 -o model_sol.cpin -op
> > model_sol.mod0.parm7 -resnums 95 188 426 517 296 -states 1 1 1 1 0
> >
> >
> > This is how my cpin file looks:
> >
> > &CNSTPH
> > CHRGDAT=-0.4157,0.2719,-0.0014,0.0876,-0.0152,0.0295,0.0295
> > ,-0.0011,-0.1906,
> > 0.1699,-0.2341,0.1656,0.3226,-0.5579,0.3992,-0.2341,0.1656,
> > -0.1906,0.1699,
> > 0.5973,-0.5679,-0.4157,0.2719,-0.0014,0.0876,-0.0858,0.
> > 019,0.019,-0.213,-0.103,
> > 0.132,-0.498,0.132,0.777,-0.814,0.0,-0.498,0.132,-0.103,0.1
> > 32,0.5973,-0.5679,
> > -0.3479,0.2747,-0.24,0.1426,-0.0094,0.0362,0.0362,0.0187,0.
> > 0103,0.0103,-0.0479,
> > 0.0621,0.0621,-0.0143,0.1135,0.1135,-0.3854,0.34,0.34,0.34,
> > 0.7341,-0.5894,
> > -0.3479,0.2747,-0.24,0.1426,-0.10961,0.034,0.034,0.06612,0.
> 01041,0.01041,
> > -0.03768,0.01155,0.01155,0.32604,-0.03358,-0.03358,-1.
> 03581,0.0,0.38604,
> > 0.38604,0.7341,-0.5894,
> > PROTCNT=0,3,
> > RESNAME='System: Unknown','Residue: TYR 95','Residue: TYR 188',
> > 'Residue: LYS 296','Residue: TYR 426','Residue: TYR 517',
> > RESSTATE=1,1,1,1,0,
> > STATEINF(0)%FIRST_ATOM=1415, STATEINF(0)%FIRST_CHARGE=0,
> > STATEINF(0)%FIRST_STATE=0, STATEINF(0)%NUM_ATOMS=21,
> > STATEINF(0)%NUM_STATES=2,
> > STATEINF(1)%FIRST_ATOM=2786, STATEINF(1)%FIRST_CHARGE=0,
> > STATEINF(1)%FIRST_STATE=0, STATEINF(1)%NUM_ATOMS=21,
> > STATEINF(1)%NUM_STATES=2,
> > STATEINF(2)%FIRST_ATOM=4476, STATEINF(2)%FIRST_CHARGE=42,
> > STATEINF(2)%FIRST_STATE=2, STATEINF(2)%NUM_ATOMS=22,
> > STATEINF(2)%NUM_STATES=2,
> > STATEINF(3)%FIRST_ATOM=6410, STATEINF(3)%FIRST_CHARGE=0,
> > STATEINF(3)%FIRST_STATE=0, STATEINF(3)%NUM_ATOMS=21,
> > STATEINF(3)%NUM_STATES=2,
> > STATEINF(4)%FIRST_ATOM=7780, STATEINF(4)%FIRST_CHARGE=0,
> > STATEINF(4)%FIRST_STATE=0, STATEINF(4)%NUM_ATOMS=21,
> > STATEINF(4)%NUM_STATES=2,
> > STATENE=0.000000,-78.199991,-0.845507,0.000000,
> > TRESCNT=5,CPHFIRST_SOL=10324, CPH_IGB=2, CPH_INTDIEL=1.0,
> > /
> >
> > I manually changed the cpin file " PROTCNT=1,0,3,2," to PROTCNT="0,3,"
> to
> > only consider deprotonated TYR and protonated LYS. Is this the right way?
> >
> >
> > After the equilibration step, *.cpout file looks like this for all time
> > steps:
> >
> > Solvent pH: 7.40000
> > Monte Carlo step size: 500
> > Time step: 500
> > Time: 1000.998
> > Residue 0 State: 0
> > Residue 1 State: 0
> > Residue 2 State: 0
> > Residue 3 State: 0
> > Residue 4 State: 0
> >
> > Residue 0 State: 0
> > Residue 1 State: 0
> > Residue 2 State: 0
> > Residue 3 State: 0
> > Residue 4 State: 0
> >
> > Residue 0 State: 0
> > Residue 1 State: 0
> > Residue 2 State: 0
> > Residue 3 State: 0
> > Residue 4 State: 0
> >
> > Residue 0 State: 0
> > Residue 1 State: 0
> > Residue 2 State: 0
> > Residue 3 State: 0
> > Residue 4 State: 0
> >
> > Does the State 0 above mean, the default state which I have mentioned in
> > the cpin file??
> >
> > Ideally, when I take any random frame after equilibration step and
> > generate a pdb, I should have the deprotonated TYR 95 atom record. But I
> > see the proton present.
> >
> > ATOM 1415 N TYR 95 50.406 44.914 56.235 1.00 0.00
> > N
> > ATOM 1416 H TYR 95 50.688 44.636 55.305 1.00 0.00
> > H
> > ATOM 1417 CA TYR 95 51.132 44.350 57.398 1.00 0.00
> > C
> > ATOM 1418 HA TYR 95 50.852 44.846 58.327 1.00 0.00
> > H
> > ATOM 1419 CB TYR 95 50.486 42.938 57.435 1.00 0.00
> > C
> > ATOM 1420 HB2 TYR 95 50.764 42.428 58.358 1.00 0.00
> > H
> > ATOM 1421 HB3 TYR 95 49.403 43.058 57.460 1.00 0.00
> > H
> > ATOM 1422 CG TYR 95 50.962 41.963 56.336 1.00 0.00
> > C
> > ATOM 1423 CD1 TYR 95 52.192 41.330 56.655 1.00 0.00
> > C
> > ATOM 1424 HD1 TYR 95 52.737 41.608 57.544 1.00 0.00
> > H
> > ATOM 1425 CE1 TYR 95 52.756 40.465 55.709 1.00 0.00
> > C
> > ATOM 1426 HE1 TYR 95 53.777 40.165 55.897 1.00 0.00
> > H
> > ATOM 1427 CZ TYR 95 52.155 40.250 54.423 1.00 0.00
> > C
> > ATOM 1428 OH TYR 95 52.880 39.621 53.479 1.00 0.00
> > O
> > ATOM 1429 HH TYR 95 52.243 39.414 52.791 1.00 0.00
> > H
> > ATOM 1430 CE2 TYR 95 50.991 40.970 54.148 1.00 0.00
> > C
> > ATOM 1431 HE2 TYR 95 50.645 41.009 53.126 1.00 0.00
> > H
> > ATOM 1432 CD2 TYR 95 50.363 41.795 55.070 1.00 0.00
> > C
> > ATOM 1433 HD2 TYR 95 49.499 42.394 54.825 1.00 0.00
> > H
> > ATOM 1434 C TYR 95 52.628 44.429 57.246 1.00 0.00
> > C
> >
> > I kindly need you're comments on this.
> >
> > Thanks
> > Regards
> > Sowmya
> > ________________________________________
> > From: Sowmya Indrakumar [soemya.kemi.dtu.dk]
> > Sent: Friday, August 18, 2017 5:24 PM
> > To: amber.ambermd.org
> > Subject: [AMBER] Deprotonation of Tyr
> >
> > Dear All,
> > I wish to perform simulations with varying salt concentration of NaCl of
> > upto 200mM at a particular pH=7. I want to keep some of the Tyrosines in
> > the deprotonated state.
> >
> > So here, my question is, Can I perform these simulations using constant
> pH
> > MD? Because, I think concentrations can be adjusted to upto 0.1M.
> >
> > Is there any other way to consider doing the deprotonation?
> > Kindly, give me you're suggestion in this regard.
> > Regards
> > Sowmya
> >
> >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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> End of AMBER Digest, Vol 2042, Issue 1
> **************************************
>
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Received on Thu Aug 31 2017 - 03:30:03 PDT
