What version of cpptraj are you using?
On Tue, Mar 15, 2016 at 6:54 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
> 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:
>
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>> 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
>> **************************************
>>
> _______________________________________________
> 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
Received on Tue Mar 15 2016 - 08:00:04 PDT
