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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Nov 18 08:16:49 CET 2013 

Hi Hari,

The .pdb file you use as input has no masses listed. Editconf then resorts
to a file called atommass.dat. You can check the format in the gromacs
share directory and put a file in the same format in the working directory.
Alternatively, you can make a run input file (.tpr) of your system and use
that as input to editconf. The .tpr file has the real masses, taken from
the atomtype definitions.

Hope it helps,

Tsjerk


On Mon, Nov 18, 2013 at 4:46 AM, Hari Pandey <harichem12 at yahoo.com> wrote:

> 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
>
>
>
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>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

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