Thank you very much Dan!
As per your suggestion, I tried as follows:
vector S1 center :1-27,65-139.CA,C,N,O
vector S2 center :28-33,46-64.CA,C,N,O
vector S3 center :140-175,265-332.CA,C,N,O
vector S4 center :176-264.CA,C,N,O
create vector_traj.nc S1 S2 S3 S4 vectraj trajfmt netcdf parmout
vector_traj.parm7 noorigin
I was expecting a pseuto-trajectory with four atoms (and one origin) but I
still get a single atom.
Thanks,
Hirdesh
On Mon, Mar 14, 2016 at 8:00 PM, <amber-request.ambermd.org> wrote:
> Send AMBER mailing list submissions to
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>
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: pseudo trajectories for 4 centers of mass? (Daniel Roe)
> 2. Re: How is ?Gnonpolar computed in MMPBSA.py in AMBER 14?
> (inp=2 in &pb namelist) (Stefan Ivanov)
> 3. Re: How is ?Gnonpolar computed in MMPBSA.py in AMBER 14?
> (inp=2 in &pb namelist) (Ray Luo)
> 4. Re: How is ?Gnonpolar computed in MMPBSA.py in AMBER 14?
> (inp=2 in &pb namelist) (Stefan Ivanov)
> 5. ISQBP 2016 meeting - registration opened! (Thomas Cheatham)
> 6. Re: AMBER:neutralisation of non integral charges (Shilpa Gupta)
> 7. Re: AMBER:neutralisation of non integral charges (Hannes Loeffler)
> 8. bad atom type with MMPBSA decomposition? (Kenneth Huang)
> 9. Re: Problems when trying to improve angle parameters whith
> paramfit (Sigurd Friis Truelsen)
> 10. Re: Problems when trying to improve angle parameters whith
> paramfit (David Cerutti)
> 11. parmed -setBond command (Balaji Selvam)
> 12. Re: parmed -setBond command (Daniel Roe)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 13 Mar 2016 14:40:39 -0600
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] pseudo trajectories for 4 centers of mass?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAAC0qOavS0Upk9-A9TbFKpo7t36+pqpX_VLga-0FeA3DL8pReg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> On Sun, Mar 13, 2016 at 11:57 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
> >
> > It would be great if I can visualize four center of masses as a "single"
> > molecule in VMD.
>
> You can do this by writing your vector data as a pseudo trajectory via
> 'vectraj', e.g.
>
> parm myparm.parm7
> trajin mytraj.nc
> vector V1 center <mask1>
> vector V2 center <mask2>
> vector V3 center <mask3>
> vector V4 center <mask4>
> create vector_traj.nc V1 V2 V3 V4 vectraj trajfmt netcdf \
> parmout vector_traj.parm7 noorigin
>
> This will create a pseudo trajectory containing your vector data. To
> ensure that this script works as-is you should use the GitHub beta
> version of cpptraj. If you want to use the AmberTools version of
> cpptraj do not include the 'noorigin' keyword since that is not yet
> implemented in that version.
>
> Hope this helps,
>
> -Dan
>
> >
> > Thanks,
> > Hirdesh
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 14 Mar 2016 02:11:01 +0000
> From: Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk>
> Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
> 14? (inp=2 in &pb namelist)
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <58F9FB3DCABE5F4F905560AB46873D7C77320B04.MBXP05.ds.man.ac.uk>
> Content-Type: text/plain; charset="iso-8859-7"
>
> Hi Prof Luo,
>
> Thank you very much for your helpful and informative reply.
>
> If I understand correctly, by default:
>
> ?Grepulsive = molecular_volume*? + c, where ? is the surface tension and c
> is the cavity offset, correct? How is the volume computed? More precisely,
> what volume is being used - solvent accessible (SAV) or solvent excluded
> volume (SEV)?
>
> As for the keywords in the output:
>
>
> EPB = ?Gelectrostatic
> ENPOLAR = ?Gattractive (?Gdispersion)
> ECAVITY = ?Grepulsive(?Gcavitation)
>
> and
>
> ?Gnonpolar = ENPOLAR + ECAVITY
>
> Finally,
>
> ?Gsolvation = ?Gnonpolar + EPB
>
> Is this correct?
>
> Best wishes,
>
> Stefan
>
>
> ________________________________________
> From: Ray Luo [rluo.uci.edu]
> Sent: Sunday, March 13, 2016 4:21 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
> 14? (inp=2 in &pb namelist)
>
> Hi Stefan,
>
> > I would like to ask a few questions regarding MMPBSA.py's
> > implementation in AMBER14. Having read the AMBER14 manual, the
> > MMPBSA.py paper, and a few papers referenced in the manual, I'm a
> > bit confused and unsure about a few things.
> >
> > What is the default scheme for computing ?Gsolvation in MMPBSA.py
> > in AMBER 14 (default is inp = 2, according to the AMBER14 manual)?
> > I'm specifically talking about the Poisson-Boltzmann computations, i.e.
> > inp=2 in the &pb namelist (which is equivalent to not specifying
> > anything for inp, because 2 is the default value, right)?. I think the
> > manual is a bit unclear. From what I understand
>
> This is correct.
>
> > ?Gsolvation = ?Gelectrostatic + ?Gnonpolar
> >
> > and
> >
> > ?Gnonpolar = ?Grepulsive(?Gcavitation) + ?Gattractive (?Gdispersion).
>
> Yes, this is correct.
>
> > Finally:
> >
> > ?Grepulsive = ?*SASA + c
>
> The default behavior is that the repulsive free energy is modeled as
> linearly depended on the volume within SASA since this is the best
> observed scheme for the tested small molecules and side chain mutation
> data.
>
> > where SASA is computed with the LCPO method. Is this correct or is
> > the cavitation term proportional to molecular volume? If so, how is that
> > computed?
>
> If you choose to model it as linearly dependent on SASA, PBSA would
> compute SASA numerically, it does not use the approximated LCPO
> method.
>
> > Here is a typical output file I get (see below). I see EPB, ENPOLAR,
> > EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is
> > the (repulsive) cavitation term and EDISPER is the (attractive)
> > dispersion term (although in this case ENPOLAR is negative and
> > ECAVITY is positive)?
>
> This is because the the printing of ECAVITY (inp=2) shares the same
> routine as the printing ENPOLAR (inp=1) in the script. Again this is
> because they both use linearly functional models. The sander printout
> is more informative.
>
> > Also, is the internal PBSA solver in sander linear or nonlinear?
>
> It's linear by default.
>
> > I have seen a lot of recommendations for the "perl" version of
> > MMPBSA, but very little for MMPBSA.py. What settings would you
> > recommend for doing Poisson-Boltzmann calculations on protein -
> > protein complexes?
>
> The two scripts should give you the same results if you use the same
> options. The difference is that the perl script uses sander, and the
> python script uses nab by default. If you prefer, you can use the
> sander option in the python script so you can choose all the &pb
> keywords as described in the manual. Apparently it is too hard to
> support all &pb keywords in either scripts.
>
> You may want to use inp=1 for protein-protein complexes because the
> inp=2 was not optimized for macromolecular "ligand" binding, though we
> are working on it.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 13 Mar 2016 20:52:30 -0700
> From: Ray Luo <rluo.uci.edu>
> Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
> 14? (inp=2 in &pb namelist)
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAOg1T6Sev165TLOpeGutcdgD4ZWnufx7Q1eYgDsx0VZCbzEyPA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Stefan,
>
> > If I understand correctly, by default:
> >
> > ?Grepulsive = molecular_volume*? + c, where ? is the surface tension and
> c is the cavity offset, correct? How is the volume computed? More
> precisely, what volume is being used - solvent accessible (SAV) or solvent
> excluded volume (SEV)?
>
> Yes, and it uses SAV since it performs better as shown in the original
> paper.
>
> > As for the keywords in the output:
> >
> > EPB = ?Gelectrostatic
> > ENPOLAR = ?Gattractive (?Gdispersion)
> > ECAVITY = ?Grepulsive(?Gcavitation)
>
> In the python script (please refer to your own output):
>
> ENPOLAR is the repulsive free energy; it's positive.
> EDISPER is the attractive free energy; it's negative.
>
> > and
> >
> > ?Gnonpolar = ENPOLAR + ECAVITY
>
> Yes.
>
> > Finally,
> >
> > ?Gsolvation = ?Gnonpolar + EPB
> >
> > Is this correct?
>
> Yes.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
> > ________________________________________
> > From: Ray Luo [rluo.uci.edu]
> > Sent: Sunday, March 13, 2016 4:21 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
> 14? (inp=2 in &pb namelist)
> >
> > Hi Stefan,
> >
> >> I would like to ask a few questions regarding MMPBSA.py's
> >> implementation in AMBER14. Having read the AMBER14 manual, the
> >> MMPBSA.py paper, and a few papers referenced in the manual, I'm a
> >> bit confused and unsure about a few things.
> >>
> >> What is the default scheme for computing ?Gsolvation in MMPBSA.py
> >> in AMBER 14 (default is inp = 2, according to the AMBER14 manual)?
> >> I'm specifically talking about the Poisson-Boltzmann computations, i.e.
> >> inp=2 in the &pb namelist (which is equivalent to not specifying
> >> anything for inp, because 2 is the default value, right)?. I think the
> >> manual is a bit unclear. From what I understand
> >
> > This is correct.
> >
> >> ?Gsolvation = ?Gelectrostatic + ?Gnonpolar
> >>
> >> and
> >>
> >> ?Gnonpolar = ?Grepulsive(?Gcavitation) + ?Gattractive (?Gdispersion).
> >
> > Yes, this is correct.
> >
> >> Finally:
> >>
> >> ?Grepulsive = ?*SASA + c
> >
> > The default behavior is that the repulsive free energy is modeled as
> > linearly depended on the volume within SASA since this is the best
> > observed scheme for the tested small molecules and side chain mutation
> > data.
> >
> >> where SASA is computed with the LCPO method. Is this correct or is
> >> the cavitation term proportional to molecular volume? If so, how is that
> >> computed?
> >
> > If you choose to model it as linearly dependent on SASA, PBSA would
> > compute SASA numerically, it does not use the approximated LCPO
> > method.
> >
> >> Here is a typical output file I get (see below). I see EPB, ENPOLAR,
> >> EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is
> >> the (repulsive) cavitation term and EDISPER is the (attractive)
> >> dispersion term (although in this case ENPOLAR is negative and
> >> ECAVITY is positive)?
> >
> > This is because the the printing of ECAVITY (inp=2) shares the same
> > routine as the printing ENPOLAR (inp=1) in the script. Again this is
> > because they both use linearly functional models. The sander printout
> > is more informative.
> >
> >> Also, is the internal PBSA solver in sander linear or nonlinear?
> >
> > It's linear by default.
> >
> >> I have seen a lot of recommendations for the "perl" version of
> >> MMPBSA, but very little for MMPBSA.py. What settings would you
> >> recommend for doing Poisson-Boltzmann calculations on protein -
> >> protein complexes?
> >
> > The two scripts should give you the same results if you use the same
> > options. The difference is that the perl script uses sander, and the
> > python script uses nab by default. If you prefer, you can use the
> > sander option in the python script so you can choose all the &pb
> > keywords as described in the manual. Apparently it is too hard to
> > support all &pb keywords in either scripts.
> >
> > You may want to use inp=1 for protein-protein complexes because the
> > inp=2 was not optimized for macromolecular "ligand" binding, though we
> > are working on it.
> >
> > All the best,
> > Ray
> > --
> > Ray Luo, Ph.D.
> > Professor
> > Biochemistry, Molecular Biophysics, Chemical Physics,
> > Chemical and Biomedical Engineering
> > University of California, Irvine, CA 92697-3900
> >
> > _______________________________________________
> > 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: 4
> Date: Mon, 14 Mar 2016 05:11:33 +0000
> From: Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk>
> Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
> 14? (inp=2 in &pb namelist)
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <58F9FB3DCABE5F4F905560AB46873D7C77320B19.MBXP05.ds.man.ac.uk>
> Content-Type: text/plain; charset="iso-8859-7"
>
> Hi Prof Luo,
>
> Many thanks and best wishes,
>
> Stefan
>
>
> ________________________________________
> From: Ray Luo [rluo.uci.edu]
> Sent: Monday, March 14, 2016 3:52 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
> 14? (inp=2 in &pb namelist)
>
> Hi Stefan,
>
> > If I understand correctly, by default:
> >
> > ?Grepulsive = molecular_volume*? + c, where ? is the surface tension and
> c is the cavity offset, correct? How is the volume computed? More
> precisely, what volume is being used - solvent accessible (SAV) or solvent
> excluded volume (SEV)?
>
> Yes, and it uses SAV since it performs better as shown in the original
> paper.
>
> > As for the keywords in the output:
> >
> > EPB = ?Gelectrostatic
> > ENPOLAR = ?Gattractive (?Gdispersion)
> > ECAVITY = ?Grepulsive(?Gcavitation)
>
> In the python script (please refer to your own output):
>
> ENPOLAR is the repulsive free energy; it's positive.
> EDISPER is the attractive free energy; it's negative.
>
> > and
> >
> > ?Gnonpolar = ENPOLAR + ECAVITY
>
> Yes.
>
> > Finally,
> >
> > ?Gsolvation = ?Gnonpolar + EPB
> >
> > Is this correct?
>
> Yes.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
> > ________________________________________
> > From: Ray Luo [rluo.uci.edu]
> > Sent: Sunday, March 13, 2016 4:21 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
> 14? (inp=2 in &pb namelist)
> >
> > Hi Stefan,
> >
> >> I would like to ask a few questions regarding MMPBSA.py's
> >> implementation in AMBER14. Having read the AMBER14 manual, the
> >> MMPBSA.py paper, and a few papers referenced in the manual, I'm a
> >> bit confused and unsure about a few things.
> >>
> >> What is the default scheme for computing ?Gsolvation in MMPBSA.py
> >> in AMBER 14 (default is inp = 2, according to the AMBER14 manual)?
> >> I'm specifically talking about the Poisson-Boltzmann computations, i.e.
> >> inp=2 in the &pb namelist (which is equivalent to not specifying
> >> anything for inp, because 2 is the default value, right)?. I think the
> >> manual is a bit unclear. From what I understand
> >
> > This is correct.
> >
> >> ?Gsolvation = ?Gelectrostatic + ?Gnonpolar
> >>
> >> and
> >>
> >> ?Gnonpolar = ?Grepulsive(?Gcavitation) + ?Gattractive (?Gdispersion).
> >
> > Yes, this is correct.
> >
> >> Finally:
> >>
> >> ?Grepulsive = ?*SASA + c
> >
> > The default behavior is that the repulsive free energy is modeled as
> > linearly depended on the volume within SASA since this is the best
> > observed scheme for the tested small molecules and side chain mutation
> > data.
> >
> >> where SASA is computed with the LCPO method. Is this correct or is
> >> the cavitation term proportional to molecular volume? If so, how is that
> >> computed?
> >
> > If you choose to model it as linearly dependent on SASA, PBSA would
> > compute SASA numerically, it does not use the approximated LCPO
> > method.
> >
> >> Here is a typical output file I get (see below). I see EPB, ENPOLAR,
> >> EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is
> >> the (repulsive) cavitation term and EDISPER is the (attractive)
> >> dispersion term (although in this case ENPOLAR is negative and
> >> ECAVITY is positive)?
> >
> > This is because the the printing of ECAVITY (inp=2) shares the same
> > routine as the printing ENPOLAR (inp=1) in the script. Again this is
> > because they both use linearly functional models. The sander printout
> > is more informative.
> >
> >> Also, is the internal PBSA solver in sander linear or nonlinear?
> >
> > It's linear by default.
> >
> >> I have seen a lot of recommendations for the "perl" version of
> >> MMPBSA, but very little for MMPBSA.py. What settings would you
> >> recommend for doing Poisson-Boltzmann calculations on protein -
> >> protein complexes?
> >
> > The two scripts should give you the same results if you use the same
> > options. The difference is that the perl script uses sander, and the
> > python script uses nab by default. If you prefer, you can use the
> > sander option in the python script so you can choose all the &pb
> > keywords as described in the manual. Apparently it is too hard to
> > support all &pb keywords in either scripts.
> >
> > You may want to use inp=1 for protein-protein complexes because the
> > inp=2 was not optimized for macromolecular "ligand" binding, though we
> > are working on it.
> >
> > All the best,
> > Ray
> > --
> > Ray Luo, Ph.D.
> > Professor
> > Biochemistry, Molecular Biophysics, Chemical Physics,
> > Chemical and Biomedical Engineering
> > University of California, Irvine, CA 92697-3900
> >
> > _______________________________________________
> > 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: 5
> Date: Sun, 13 Mar 2016 23:15:46 -0600 (MDT)
> From: Thomas Cheatham <tec3.utah.edu>
> Subject: [AMBER] ISQBP 2016 meeting - registration opened!
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <alpine.OSX.2.20.1603132314110.7776.thomass-macbook-air-3.local>
> Content-Type: text/plain; charset="iso-8859-15"
>
>
> ...opportunities for people to speak! --tec3
>
>
> Dear colleagues,?
>
> We are thrilled to announce that the registration for the President's
> Meeting 2016 of the International Society of Quantum Biology and
> Pharmacology (ISQBP) is now opened!?
>
> The program will feature oral presentations by an exciting line up of
> invited speakers (see list below). In addition we welcome abstract
> submission for ca. 15 short oral presentations and ?posters, with a focus
> on the following topics: nucleic acids, enzyme catalysis, protein-lipid
> interactions, methods development, protein dynamics and drug design.?
>
> Registration and abstract submission forms can be found
> at?www.isqbp2016.org.
>
> DATE: 19-22 June 2016?
>
> PLACE: Grand Hotel Terminus, Bergen, Norway (www.grandterminus.no/en/).
> The venue is conveniently located in the city center of Bergen, with
> frequent transfer from the airport (30 minutes drive by airport bus or
> taxi).
>
> INVITED SPEAKERS: Charles L. Brooks III, Thomas E. Cheatham III, Vlad
> Cojoracu, Annick Dejaegere, Carmen Domene, William L. Jorgensen, Syma
> Khalid, Carmay Lim, Alex MacKerell, Lennart Nilsson, Masha Niv, Modesto
> Orozco, Montgomery Pettitt, Carol Post, Rebecca Wade
>
> ABSTRACTS: we are welcoming abstracts for ca. 15 short oral presentations
> and posters.
>
> IMPORTANT DATES:
> Early bird registration until March 20th
> Abstract submission deadline for talks: March 20th
> Abstract submission deadline for posters: April 15th
>
> TRAVEL AWARDS: Two ISQBP travel awards will be provided by the Society to
> support students presenting their work at the meeting. The selection will
> be based on the creativity, relevance and quality of the work as well as
> the distance the student has to travel to attend the conference.
>
> MEETING WEBSITE:?www.isqbp2016.org
>
> ISQBP: want to know more about the International Society of Quantum
> Biology and Pharmacology? Visit our webpage at?http://isqbp.umaryland.edu
>
>
>
>
> With best regards,
> The Scientific Committee
>
> Nathalie Reuter?
> (Computational Biology Unit, University of Bergen)
>
> Bjorn Olav Brandsdal?
> (Centre for Theoretical and Computational Chemistry, University of Tromso)
>
> Michele Cascella
> (Centre for Theoretical and Computational Chemistry, University of Oslo)To
> join or leave the
> molecular-dynamics-news email list, go to:
> http://www.jiscmail.ac.uk/lists/molecular-dynamics-news.html
>
> ------------------------------
>
> Message: 6
> Date: Mon, 14 Mar 2016 13:22:42 +0000 (UTC)
> From: Shilpa Gupta <guptashilpa_91.yahoo.com>
> Subject: Re: [AMBER] AMBER:neutralisation of non integral charges
> To: <amber.ambermd.org>
> Message-ID:
> <2032101966.923925.1457961762365.JavaMail.yahoo.mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Amber users,
> i am getting non integral charges (19.994) on my macromolecule. How
> can i neutralise the charge using addions in tleap. Thanks in advance.
>
>
> Shilpa Gupta
> University of Delhi
>
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 14 Mar 2016 13:37:42 +0000
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] AMBER:neutralisation of non integral charges
> To: <amber.ambermd.org>
> Cc: Shilpa Gupta <guptashilpa_91.yahoo.com>
> Message-ID: <20160314133742.6d9c6ecb.zgb83773vig.dl.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> On Mon, 14 Mar 2016 13:22:42 +0000
> Shilpa Gupta <guptashilpa_91.yahoo.com> wrote:
>
> > Dear Amber users,
> > i am getting non integral charges (19.994) on my macromolecule.
> > How can i neutralise the charge using addions in tleap. Thanks in
> > advance.
>
> Type 'help addions' in leap and read the manual. I spotted an example
> in the latter when I searched for 'neutralize'.
>
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 14 Mar 2016 09:58:25 -0400
> From: Kenneth Huang <kennethneltharion.gmail.com>
> Subject: [AMBER] bad atom type with MMPBSA decomposition?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CALeh7kBZ2duQo0Eg2y2W0q_-rj-NBXufVcgSA3eAgk14NrcTjA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi all,
>
> As the subject says, I'm running into a bad atom type error with MMPBSA.
> Specifically when I try to run decomposition- without decomposition, it
> runs without any errors, but when I try to run decomp it exits after
> initializing with the bad atom type error.
>
> I already had two modifications in mdread2.F90 which I thought would've
> fixed the issue-
>
> ! Begin modifications
> > else if (atype == 'K+') then
> > x(l165-1+i) = 1.52d0 + 1.4d0
> > x(l170-1+i) = 0.68563d0
> > x(l175-1+i) = -0.1868d0
> > x(l180-1+i) = -0.00135573d0
> > x(l185-1+i) = 0.00023743d0
> > ! End modifications
> >
>
>
> else if (atomicnumber .eq. 12) then
> > ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys.
> > 1997, 107, 5422
> > ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys.
> > 1997, 107, 5422
> > ! Mg radius = 1.45A: Aqvist 1992
> > x(L165-1+i) = 1.18d0 + 1.4d0
> > ! Begin modifications
> > else if (atomicnumber .eq. 19) then
> > x(L165-1+i) = 1.52d0 + 1.4d0
> > ! End modifications
> > else
> > write( 0,* ) 'bad atom type: ',atype,' cannot perform
> >
>
> And I've double checked %FLAG ATOMIC_NUMBER in the topology files to make
> sure that the atomic number is correct (19), did a fresh install and
> recompiled in serial and parallel with the changes to mdread2.f90, but I'm
> still getting the same error with my input as-
>
> &general
> endframe=1000, interval=100, keep_files=2, verbose=1,
> receptor_mask=':1-1044', ligand_mask=':1045-2088'
> /
> &gb
> igb=2, saltcon=0.100,
> /
> &pb
> istrng=0.100, indi=2.0, radiopt=0, inp=1,
> /
> &decomp
> idecomp=1, print_res="12-24; 291-308; 330-342; 365-389"
> dec_verbose=3,
> /
>
> At this point, I'm kind of baffled as to why it'd throwing up the error
> message since I can't find a discernible reason why it'd be tossing out
> that message.
>
> Best,
>
> Kenneth
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
>
>
> ------------------------------
>
> Message: 9
> Date: Mon, 14 Mar 2016 15:28:52 +0000
> From: Sigurd Friis Truelsen <sigut.env.dtu.dk>
> Subject: Re: [AMBER] Problems when trying to improve angle parameters
> whith paramfit
> To: AMBER Mailing List <amber.ambermd.org>
> Cc: "jeremie.knoops.umons.ac.be" <jeremie.knoops.umons.ac.be>
> Message-ID:
> <
> AFC3EDD6C86AD140AA9454795CA43DB20189CD84.ait-pex02mbx04.win.dtu.dk>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear J?r?mie and Amber Users,
>
> >Dear Amber Users,
> >
> >I'm trying to improve angle parameters but paramfit seems not able to
> read angle parameters from the file which specify the parameters to fit.
> >This looks like an old issue that seems to have been fixed (
> http://archive.ambermd.org/201407/0481.html) , but I'm using Ambertools
> 15.
> >When I specify only angle parameters, I get this message : ERROR IN MAIN
> - NDIMENSIONS VALUE OF 0 IS LESS THAN 1
> >How to fix this bug?
> >
> >Thanks,
> >
> >J?r?mie Knoops
>
> I have the same problem when trying to fit angle parameters defined in a
> file. If only angles are to be fitted I get the ERROR message like yours.
> If I specify to fit everything in the file, Paramfit will perform the fit
> on bonds and dihedrals, but not on the angles.
> The only way I can get the angles to be fitted is to set
> "PARAMETERS_TO_FIT" to "DEFAULT", and all parameters will be fitted, but
> this is not necessarily desired.
> Did you find a solution for this problem?
>
> Best regards,
>
> Sigurd Truelsen
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 10
> Date: Mon, 14 Mar 2016 12:42:53 -0400
> From: David Cerutti <dscerutti.gmail.com>
> Subject: Re: [AMBER] Problems when trying to improve angle parameters
> whith paramfit
> To: AMBER Mailing List <amber.ambermd.org>
> Cc: "jeremie.knoops.umons.ac.be" <jeremie.knoops.umons.ac.be>
> Message-ID:
> <CAEmzWj1jJceVTCnCSuWkDAGQ5xy1eqr=
> BBHeQrjRfvTTK5GrJQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Not sure what paramfit does with angle parameterization, but you should
> both give mdgx a shot. It's not enough to just reoptimize the stiffnesses
> of the angle parameters, you need to get the equilibria in there as well.
> mdgx has the capability to do it all, plus any torsions you want, in a
> single run, so long as you have coordinates, energies, and an Amber
> topology for your system I can show you how to run the calculations.
> Really should get a parameter development tutorial for mdgx up on the
> website.
>
> Dave
>
>
> On Mon, Mar 14, 2016 at 11:28 AM, Sigurd Friis Truelsen <sigut.env.dtu.dk>
> wrote:
>
> > Dear J?r?mie and Amber Users,
> >
> > >Dear Amber Users,
> > >
> > >I'm trying to improve angle parameters but paramfit seems not able to
> > read angle parameters from the file which specify the parameters to fit.
> > >This looks like an old issue that seems to have been fixed (
> > http://archive.ambermd.org/201407/0481.html) , but I'm using Ambertools
> > 15.
> > >When I specify only angle parameters, I get this message : ERROR IN
> MAIN
> > - NDIMENSIONS VALUE OF 0 IS LESS THAN 1
> > >How to fix this bug?
> > >
> > >Thanks,
> > >
> > >J?r?mie Knoops
> >
> > I have the same problem when trying to fit angle parameters defined in a
> > file. If only angles are to be fitted I get the ERROR message like yours.
> > If I specify to fit everything in the file, Paramfit will perform the fit
> > on bonds and dihedrals, but not on the angles.
> > The only way I can get the angles to be fitted is to set
> > "PARAMETERS_TO_FIT" to "DEFAULT", and all parameters will be fitted, but
> > this is not necessarily desired.
> > Did you find a solution for this problem?
> >
> > Best regards,
> >
> > Sigurd Truelsen
> >
> > _______________________________________________
> > 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: Mon, 14 Mar 2016 13:19:39 -0500
> From: Balaji Selvam <bselvam01.gmail.com>
> Subject: [AMBER] parmed -setBond command
> To: amber.ambermd.org
> Message-ID:
> <
> CAMwUL-YMD3fdBRh+XXzGoksWd5wknCOCNZmdc0027zMA3hxgFA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear AMBER Users,
>
> I am trying to fix the OH bond length of the residue using parmed setBond
> command.
>
> I am using the following script
>
> parmed.py example.prmtop
>
> loadRestrt 99.rst
>
> setOverwrite True
>
> setBond :640.OG1 :640.HG1 100 0.96
>
> outparm test.prmtop test01.rst
>
>
> 640 is the residue number, 100 is the force constant and 0.96 is the actual
> bond length.
>
>
> I am not changing the bond just trying the fix the actual bond length using
> parmed.
>
>
> However, the script shows error as "AmberMask: Unrecognized symbol in
> residue name parsing".
>
>
> Kindly advice.
>
>
> Many Thanks
>
> Balaji
>
>
> ------------------------------
>
> Message: 12
> Date: Mon, 14 Mar 2016 12:36:04 -0600
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] parmed -setBond command
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qOYtSrwuwWW7HwfY4Ctrdr9iUOM=
> HdN7e_rK4gzVZx3k6w.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Mar 14, 2016 at 12:19 PM, Balaji Selvam <bselvam01.gmail.com>
> wrote:
> > setBond :640.OG1 :640.HG1 100 0.96
>
> These are not valid Amber masks. The symbol for atom is '.', not '.'.
>
> ":640.OG1" etc will work. You may want to review Amber mask syntax;
> see sections 20.1 or 29.1.6 in the Amber15 manual.
>
> -Dan
>
> >
> > outparm test.prmtop test01.rst
> >
> >
> > 640 is the residue number, 100 is the force constant and 0.96 is the
> actual
> > bond length.
> >
> >
> > I am not changing the bond just trying the fix the actual bond length
> using
> > parmed.
> >
> >
> > However, the script shows error as "AmberMask: Unrecognized symbol in
> > residue name parsing".
> >
> >
> > Kindly advice.
> >
> >
> > Many Thanks
> >
> > Balaji
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 1515, Issue 1
> **************************************
>
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Received on Tue Mar 15 2016 - 06:00:05 PDT
