[gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 69

Mon Nov 18 04:49:30 CET 2013

Dear Gromacs users:
I am hanging on the problems with editconf: can any one , please help me:
my problem is editconf displays wrong value of mass of input:
In Last post JUSTIN pointed out that he got correct value, while he run  , but let me post all about my problem:
My atomtypes.atp  has only two atoms( I make it)
H       1.00800 
SOD     22.99
My aminoacids.rtp has two rasidues
[ SOD ]
  [ atoms ]
        SOD    SOD      1       1
[ AIT ]
  [ atoms ]
        H1     H       1       0
my aa.pdb has three atoms
ATOM      1  H1  AIT     1      14.328 -11.667   1.544  1.00  0.00
ATOM      2  H2  AIT     1      15.013 -11.434   0.080  1.00  0.00
ATOM      3  SOD SOD     2       5.599   4.582   0.028  1.00  0.00
For testing purpose I used : pdb2gmx -f aa.pdb -o aaa.pdb and I have following:
ATOM      1  H1  AIT     1      14.328 -11.667   1.544  1.00  0.00           H
ATOM      2  H2  AIT     1      15.013 -11.434   0.080  1.00  0.00           H
ATOM      3  SOD SOD     2       5.599   4.582   0.028  1.00  0.00         S
Clearly Gromacs updating my SOD atom as S atom 
When I do editconf :::  editconf -f aaa.pdb -o aa.gro -density 10000; it showing following output with incorrect result. I did -density because I need density of input for my research:

WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.

Volume  of input 1.728 (nm^3)
Mass    of input 34.0809 (a.m.u.) ( here we can see that gromacs is taking sulphur atoms mass rather that mass os SOD
Density of input 32.7504 (g/l)
Scaling all box vectors by 0.319943
new system size :  0.301  0.520  0.049
new center      :  0.373 -0.198  0.018 (nm)
new box vectors :  0.384  0.384  0.384 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :   0.06               (nm^3)

I tried every possibilities. I updated name of atoms in all files , .pdb .atp and .rtp everywhere. butt no benifit. SOMEBODY HELP ME PLEASE. What might be its reason. Do I have to do something in source code or may be OS plateforms any any possibility. PLEASE HELP ME. THIS ERROR IS HANGING ME SINCE A MONTH.If I have to do something in source code please let me know which file should be that. Or if it is due to environment then please let me know how do I come over this problem..
I tried alot. I rebooted my computer, I re installed gcc 4.8.2, Cmake latest, git , FFTW3, all and finally gromacs 4.6.4 very recent release but still the problem not gone away.  Please help me

Thanks in advance

On Sunday, November 17, 2013 3:01 AM, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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Today's Topics:

   1. Re: How to construct mixed lipid bilayer (Bj?rn Sommer)
      (Bj?rn Sommer)
   2. Re: gromacs.org_gmx-users Digest, Vol 115, Issue 68
      (Raghunath Satpathy)
   3. Re: simulated annealing (Justin Lemkul)

----------------------------------------------------------------------

Message: 1
Date: Sat, 16 Nov 2013 23:29:40 +0100
From: Bj?rn Sommer <bjoern at CELLmicrocosmos.org>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] How to construct mixed lipid bilayer (Bj?rn
    Sommer)
Message-ID:
    <11315_1384640977_ZZi0C2t2LMOzM.00_5287F1D4.7030406 at CELLmicrocosmos.org>

Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Am 13.11.2013 14:51, schrieb gmx-users-request at gromacs.org:
> Message: 4
> Date: Wed, 13 Nov 2013 18:44:08 +0530
> From: Nikhil Agrawal<nikhil.08oct at gmail.com>
> Subject: [gmx-users] How to construct mixed lipid bilayer
> To:gmx-users at gromacs.org
> Message-ID:
> <CAC4R+aJPnMFmn-RV=uGgL+hNSPauDYOkYiiJVKew0s22YRrMWQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear All,
>
> can anyone tell me how to construct mixed lipid bilayer in gromacs
>
> id possible also provide me the command to construct the mixed bilayer
>
>
> Thanks in advance
>
> Nikhil

[Second try, my first mail seems to got lost due to mailing list migration]

Dear Nikhil,

especially for heterogeneous bilayers our MembraneEditor was developed, 
you can download it here:

http://Cm2.CELLmicrocosmos.org

It is Java Webstart, so it is quite easy to use and install, but you can 
also download the source code in the forum.

Here you find some videos about how to use it:

http://cellmicrocosmos.org/index.php/videos

We also use it with Gromacs. There is no pre-euqilibration done in the 
MembraneEditor. But we never needed it, because the equilibration with 
Gromacs works very good.

If you have further question, just let me know. A new version with a 
number of improvements is coming during the next month!

Best wishes,
Bj?rn

------------------------------

Message: 2
Date: 17 Nov 2013 01:14:34 -0000
From: "Raghunath Satpathy" <satpathyr at rediffmail.com>
To: <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue
    68
Message-ID:
    <1384599990.S.7323.1575.H.Tmdyb21hY3Mub3JnX2dteC11c2Vycy1yZXF1ZXN0QABncm9tYWNzLm9yZ19nbXgtdXNlcnMgRGlnZXN0LCA_.RU.rfs278,    
    rfs278, 649,
    412.f5-224-140.old.1384650874.21735 at webmail.rediffmail.com>
Content-Type: text/plain; charset="UTF-8"

is it necessary to heat and cool protein in simulated annealing ? i wanna to check thermostability by md simulation only by increasing temp (without cooling ) in many picoseconds , is it possible to get good result ? pls reply soon 

------------------------------

Message: 3
Date: Sat, 16 Nov 2013 20:31:15 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users
    <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] simulated annealing
Message-ID: <52881C63.6000100 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Please use a descriptive subject line.

On 11/16/13 8:14 PM, Raghunath Satpathy wrote:
>
>
> is it necessary to heat and cool protein in simulated annealing ? i wanna to check thermostability by md simulation only by increasing temp (without cooling ) in many picoseconds , is it possible to get good result ? pls reply soon
>

What is "necessary" depends on what you are trying to achieve.  See what others 
do in the literature and develop a protocol based on what seems sensible.  For 
thermostability assessments, I don't see any immediate need to cycle 
temperatures up and down.  Simple heating could be perfectly reasonable.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================

------------------------------

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End of gromacs.org_gmx-users Digest, Vol 115, Issue 69
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