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, <[email protected]
<mailto:[email protected]>> wrote:
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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: " ??? " <[email protected] <mailto:[email protected]>>
Subject: [gmx-users] freeze backbone & Pressure scaling error
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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 <[email protected]
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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 <[email protected]
<mailto:[email protected]>>
Subject: Re: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and
opls_180 (OS)
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
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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 <[email protected]
<mailto:[email protected]>>
Subject: Re: [gmx-users] Freeze backbone & Pressure scaling more than
1%
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
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 <[email protected]
<mailto:[email protected]>>
Subject: [gmx-users] Hi
To: [email protected] <mailto:[email protected]>
Message-ID:
<[email protected]
<mailto:[email protected]>>
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 <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] Hi
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
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
*****************************************
--
--------------------------------------------------------------------------------------------------
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: [email protected] <mailto:[email protected]>
------------------------------------------------------------------------------------------------------
"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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