[gmx-users] Re: Regarding g_rmsf
Justin A. Lemkul
jalemkul at vt.edu
Tue Dec 15 14:32:18 CET 2009
rituraj purohit wrote:
> Hi,
> I simulated one crystallize protein (from pdb) having amino acid entry
> from 24 to 740. 1 to 23 residues was missing.
>
> When i am plotting RMSF for each residues by following command
> g_rmsf -f md.tpr -s md.trr (with the help of Grace)
>
> I am getting plot from 1 to 717 residues. I Think in prior step of
> simulation, gromacs changed the residues number of original pdb file and
> allotted the new number, that why residue 24 now become residue 1.
>
This is true.
> I want to analyze RMSF at the spacific residue 340 from pdb entry but
> after simulation it become 317. Their is no problem in analysing RMSF
> value at 317 but actual problem in potting it is comming 340.
>
I don't understand your problem. If you know what the re-numbered residue
actually is, why is there a problem at all?
> My question is that How i can plot RMSF from residue number 24 to 740,
> Which is actually in PDB file.
>
Write a script that re-numbers your .xvg file, which you may even be able to do
within Grace, as well.
-Justin
> Regards
> Rituraj
>
>
>
>
>
> On Tue, Dec 15, 2009 at 4:30 PM, <gmx-users-request at gromacs.org
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> Today's Topics:
>
> 1. freeze backbone & Pressure scaling error ( ??? )
> 2. typo in ffoplsaanb.itp for opls_179 (OS) and opls_180 (OS)
> (Pradip Biswas)
> 3. Re: typo in ffoplsaanb.itp for opls_179 (OS) and opls_180
> (OS) (Mark Abraham)
> 4. Re: Freeze backbone & Pressure scaling more than 1%
> (Mark Abraham)
> 5. Hi (ashish pandey)
> 6. Re: Hi (XAvier Periole)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 15 Dec 2009 13:56:44 +0900 (KST)
> From: " ??? " <chemgirl at hanmail.net <mailto:chemgirl at hanmail.net>>
> Subject: [gmx-users] freeze backbone & Pressure scaling error
> To: "gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>"
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> Message-ID:
>
> <20091215135644.HM.E000000000Fwt4s at chemgirl.wwl1109.hanmail.net
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> ------------------------------
>
> Message: 2
> Date: Mon, 14 Dec 2009 23:00:30 -0600
> From: Pradip Biswas <biswas.pk <http://biswas.pk>@gmail.com
> <http://gmail.com>>
> Subject: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and
> opls_180 (OS)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
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> <2301c61d0912142100g675259cfxd374d9adaacff093 at mail.gmail.com
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>
> Hi,
>
> The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are
> typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while
> doing QMMM,
> these oxygen atoms are being recognized as Nitrogen atoms.
>
> Biswas.
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> ------------------------------
>
> Message: 3
> Date: Tue, 15 Dec 2009 16:33:28 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
> Subject: Re: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and
> opls_180 (OS)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4B271FA8.2030309 at anu.edu.au
> <mailto:4B271FA8.2030309 at anu.edu.au>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Pradip Biswas wrote:
> > Hi,
> >
> > The atomic numbers of the atom types opls_179 (OS) and opls_180
> (OS) are
> > typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while
> doing
> > QMMM, these oxygen atoms are being recognized as Nitrogen atoms.
>
> DvdS fixed this in the git source earlier this week.
>
> Mark
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 15 Dec 2009 16:36:10 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
> Subject: Re: [gmx-users] Freeze backbone & Pressure scaling more than
> 1%
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4B27204A.3030602 at anu.edu.au
> <mailto:4B27204A.3030602 at anu.edu.au>>
> Content-Type: text/plain; charset=EUC-KR
>
> 이진희 wrote:
> >
> >
> > Dear all
> >
> >
> >
> > When I run produnction run using freeze backbone in GROMACS
> 4.0.5, the
> > error was shown.
> >
> > But I didn't use freeze backboone, the error wasn't shown.
> >
> > ------------------------------------------------
> >
> > Step 1 Warning: Pressure scaling more than 1%.
> >
> > ------------------------------------------------
> >
> > I changed "tau_p" value from 0.5 to 5 in md.mdp file, but the above
> > error was shown.
> >
> > I don't know how to solve it. Any one give some advice.
>
> Provide a full description. What's the system, how big is it, how did
> you equilibrate it, why/how are you freezing the backbone, does the run
> finish, does the trajectory look ok?
>
> Mark
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 15 Dec 2009 14:22:39 +0530
> From: ashish pandey <ashishpandey12 at gmail.com
> <mailto:ashishpandey12 at gmail.com>>
> Subject: [gmx-users] Hi
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID:
> <f2be40f50912150052l6f04594ct5817933f4bae8e4a at mail.gmail.com
> <mailto:f2be40f50912150052l6f04594ct5817933f4bae8e4a at mail.gmail.com>>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all,
> my self ashish and i am trying to dynamics using gromacs.
> i am new in these field. in the time of running Pdb2gmx to create .gro
> file. i am geting these error.
>
> Fatal error:
> Atom HA in residue MET 1 not found in rtp entry with 9 atoms
>
> please help me sortout these problem.
>
> --
> Ashish Pandey
> NIPER India
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 15 Dec 2009 10:03:29 +0100
> From: XAvier Periole <x.periole at rug.nl <mailto:x.periole at rug.nl>>
> Subject: Re: [gmx-users] Hi
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <F925B208-9BF1-4C79-AC31-58E22B739B37 at rug.nl
> <mailto:F925B208-9BF1-4C79-AC31-58E22B739B37 at rug.nl>>
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>
>
> try the option -ignh, it will ignore the the hydrogen atoms in your
> pdb file and generate the ones necessary to the force field you choose.
>
> On Dec 15, 2009, at 9:52 AM, ashish pandey wrote:
>
> > Dear all,
> > my self ashish and i am trying to dynamics using gromacs.
> > i am new in these field. in the time of running Pdb2gmx to create
> .gro
> > file. i am geting these error.
> >
> > Fatal error:
> > Atom HA in residue MET 1 not found in rtp entry with 9 atoms
> >
> > please help me sortout these problem.
> >
> > --
> > Ashish Pandey
> > NIPER India
> > --
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> End of gmx-users Digest, Vol 68, Issue 77
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> --
> --------------------------------------------------------------------------------------------------
> RITURAJ PUROHIT
> Assistant Professor, Bioinformatics Division
> School of Bio-sciences and Technology (SBST)
> Vellore Institute of Technology, University
> Address: SBST, VIT University, Vellore-632014,Tamilnadu, India.
> Phone: +91-416-2202638 (Lab), +91-9944649073 (Mobile)
> Fax; +91-416-2243092, E-mail: rituraj at vit.ac.in <mailto:rituraj at vit.ac.in>
> ------------------------------------------------------------------------------------------------------
> "The future belongs to those who believe in the beauty of their dreams."
> --------------------------------------------------------------------------------------------------------
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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