[gmx-users] simulating dimer proteins

delara aghaie d_aghaie at yahoo.com
Sat Jun 16 13:33:25 CEST 2012 

Dear Justin
Hello :)
Thanks for your response. 

You have mentioned that "Position restraints are applied per [moleculetype], as indicated 
in the topology". 

In my topol.top file there are two .itp files included for the two protein chains. I opened the following file:topol_Protein_chain_A.itp
Here I have :
---------------

[ moleculetype ]
; Name            nrexcl
Protein_chain_A     3
---------------
1)))))) The molecultype has not mentioned explicitly protein as it is required by tc_grps (Protein non-Protein). Does gromacs recognizes (Protein_chain_A) as protein and so gives special thermostat to it????
=====================================
for the 1RFB protein having two chains, I did energy minimization and then NVT simulation for 200 ps and then used g_energy command to plot temperature.
using this command line:
g_energy -f nvt.mdp -o temp.xvg    and then select 15   0   for temperature::::

Then it gives me temp.xvg output, but some warning are written on the screen. You can see them below:

------Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Temperature                 309.834       0.17    3.51504   0.945045  (K)

You may want to use the -driftcorr flag in order to correct
for spurious drift in the graphs. Note that this is not
a substitute for proper equilibration and sampling!

2----((what is the reason for spurious drist and is it necessary to be corrected?))

WARNING: nmol = 1, this may not be what you want.
(I do not understand this warning)

Temperature dependent fluctuation properties at T = 309.834.

Heat capacities obtained from fluctuations do *not* include
quantum corrections. If you want to get a more accurate estimate
please use the g_dos program.
3-----(It has mentioned that this program needs alot of memory. Is it really necessary to do this?)

WARNING: Please verify that your simulations are converged and perform
a block-averaging error analysis (not implemented in g_energy yet)

4------(What should I do for this warning)???

========================================================
5----Although the two chains of my protein are identical, does it make trouble to have two separate .itp files for them? pdb2gmx with the option (chainsep) has given these two .itp files to me.




Thanks alot for your valuable time....
Regards 

Delara






________________________________
 From: Justin A. Lemkul <jalemkul at vt.edu>
To: delara aghaie <d_aghaie at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, 16 June 2012, 15:37
Subject: Re: [gmx-users] simulating dimer proteins
 


On 6/16/12 6:29 AM, delara aghaie wrote:
> Dear Mark
> Again some questions:
> ------------------------------------------
> I used -chainsep option to pdb2gmx and generated topology files for two protein
> chains and also .gro file containing both chains
> ........................................
> The energy minimization was done successfully and I got average pot.
> energy=-1.2*10^6
> Then I started NVT simulation for 200 ps with position restraints on proteins.
>
> 1)) having the following line in .mdp file will do position restraints on both
> chains, considering that each chan has its own .top file????

Yes, it does.  Position restraints are applied per [moleculetype], as indicated 
in the topology.

> define          = -DPOSRES      ; position restrain the protein
> ---------------------------------
> 200 ps, NVT simulation finished, but I think there is something wrong here. This
> is part of my nvt.mdp file:
>
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = Protein Non-Protein   ; two coupling groups - more accurate
> tau_t           = 0.1   0.1     ; time constant, in ps
> ref_t           = 310   310     ; reference temperature, one for each group, in K
>
> As here my protein has two chains, is it necessary to increase the tc-groups???

No.  See the following:

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do

-Justin

> I mean should I use for example
> tc-grps = Protein_chain_A Protein_chain_B SOl NA     (These are the names that
> are present at the end of topol.top file)
>
> Thanks
> Regards
> D.M
>
>
> --------------------------------------------------------------------------------
>
>
>
> --------------------------------------------------------------------------------
>
>
> *From:* Mark Abraham <Mark.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Saturday, 16 June 2012, 12:15
> *Subject:* Re: [gmx-users] simulating dimer proteins
>
> On 16/06/2012 5:31 PM, delara aghaie wrote:
>> Dear Gromacs Users
>>
>> Running pdb2gmx on a pdb file containing a dimer protein, I used option ((
>> chainsep id_or_ter)))
>> This resulted in separated topologies for each chain and separated posre
>> files. Also in the .gro file, the aminoacides of the second chain started from
>> number 1. (Without this option the second chain aminoacides will receive
>> numbers in continuation of numbers of first chain))....
>>
>> Now:
>> Can I use these files to continue the simulations or again it is necessary to
>> follow the procedure explained in multiple chains gromacs???
>>
>
> By definition of pdb2gmx function, you now have a topology and a coordinate file
> that matches. That is the minimum requirement for grompp to succeed later.
> grompp doesn't care about some aspects of atom numbering - including your
> observation above.
>
> Mark
>
> --
> gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
> before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
> before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120616/b484e224/attachment.html>

More information about the gromacs.org_gmx-users mailing list