[gmx-users] Re: Not enough ref_t and tau_t values
Sriprajak Krongsuk
sprajakk at yahoo.com
Mon Aug 29 12:17:32 CEST 2005
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> Today's Topics:
>
> 1. error: Not enough ref_t and tau_t values!
> (Prettina Anto_Louis)
> 2. Re: Simulation crashing (Tsjerk Wassenaar)
> 3. difficulty when I run mdrun (Rahul Karyappa)
> 4. Re: difficulty when I run mdrun (Magnus
> Andersson)
>
>
>
----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 29 Aug 2005 00:35:08 -0700 (PDT)
> From: Prettina Anto_Louis <pretti_louis at krify.com>
> Subject: [gmx-users] error: Not enough ref_t and
> tau_t values!
> To: gmx-users at gromacs.org
> Message-ID:
> <20050829003508.F702DB at dm22.mta.everyone.net>
> Content-Type: text/plain
>
> Hello gromacs users!
>
> Greetings!
>
>
>
> I was running simulation of a protein with a ligand.
> I have created the topology for the ligand molecule
> with the help of PRODRG server and ran energy
> minimisation step successfully. But while I am
> running
> grompp before the mdrun program it is giving
> following
> error:
> Making dummy/rest group for T-Coupling containing 20
> elements
> Fatal error: Not enough ref_t and tau_t values!
>
> Can you please tell me why I am getting such an
> error? Also what are ref_t and tau_t values?
>
> I encountered the following error after grompp:
> ------------------------------------------
> processing coordinates...
> Shuffling coordinates...
> Entering shuffle_xv
> Sorting coordinates for 1 copies of molecule
> Protein_A
> Sorting coordinates for 9896 copies of molecule SOL
> Sorting coordinates for 0 copies of molecule K
> Sorting coordinates for 0 copies of molecule Na
> Sorting coordinates for 0 copies of molecule Ca
> Sorting coordinates for 0 copies of molecule Mg
> Sorting coordinates for 0 copies of molecule Cl
> Sorting coordinates for 0 copies of molecule Zn
> Sorting coordinates for 1 copies of molecule FRA
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (OW - HW1)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW1 - HW2)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW2 - OW)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (OW - HW1)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW1 - HW2)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW2 - OW)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (OW - HW1)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW1 - HW2)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW2 - OW)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (OW - HW1)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW1 - HW2)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW2 - OW)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (OW - HW1)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW1 - HW2)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW2 - OW)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (OW - HW1)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW1 - HW2)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW2 - OW)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (OW - HW1)
> Warning: atom names in pla_drg.top and after_em.gro
> don't match (HW1 - HW2)
> (more than 20 non-matching atom names)
> WARNING 2 [file "pla_drg.top", line 8006]:
> 14236 non-matching atom names
> atom names from pla_drg.top will be used
> atom names from after_em.gro will be ingnored
>
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> # ANGLES: 7484
> # PDIHS: 3470
> # IDIHS: 3180
> # LJ14: 6948
> # CONSTR: 3840
> # SETTLE: 19792
> Walking down the molecule graph to make shake-blocks
> initialising group options...
> processing index file...
> Analysing residue names:
> Opening library file
> /opt/soft/gromacs/share/top/aminoacids.dat
> There are: 9898 OTHER residues
> There are: 123 PROTEIN residues
> There are: 0 DNA residues
> Analysing Protein...
> Analysing Other...
> Making dummy/rest group for T-Coupling containing 20
> elements
> Fatal error: Not enough ref_t and tau_t values!
>
> -----------
>
>
> thanking you!
>
>
>
>
>
>
>
>
>
> "praise the lord!"
>
>
> With prayers,
> prettina
>
>
>
I think if you rewrite atom type correctly as warning,
you will be successful to run grompp command
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>
> ------------------------------
>
> Message: 2
> Date: Mon, 29 Aug 2005 09:17:25 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Simulation crashing
> To: Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <8ff89815050829011778007c6 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Bob,
>
> Just try
> trjconv -f initial.g96 -s initial.g96 -o initial.pdb
> -pbc inbox
> and have a look at the structure with rasmol, pymol
> or any other *mol;
> you'll see that you have severe overlaps, which will
> cause the system
> to explode. You can't do something like this just by
> pasting in some
> extra molecules!
>
> What you should do is extend your box to create a
> vacuum layer, and
> fill that with methanol. Don't forget to first do
> energy minimization.
>
>
=== message truncated ===
Mr. Sriprajak Krongsuk
Physics Department
Faculty of Science
Mahidol University
Bangkok, Thailand 10400
E-Mail: sriprajak at hotmail.com
sprajakk at yahoo.com
Tel. 01-2620095
^^^ ^^^
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