[gmx-users] Simulated annealing MD

[chandran karunakaran]

Hi,

  I am interested in simulated annealing MD
for studying the protein-drug interactions.
Does any body have optimized paramters for
running using GMX? 

With thanks
Dr.C.Karunakaran


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> Today's Topics:
> 
>    1. Fatal Error: UNK (Amol D. Atre)
>    2. Re: gmx-users Digest, Vol 17, Issue 63 (Jozef
> Hritz)
>    3. second line in rtp (Jozef Hritz)
>    4. Re: Fatal Error: UNK (MGi?)
>    5. crystal ligand-protein complex (Alberto
> Malvezzi)
>    6. umbrella pull code (Christian Schauz)
>    7. Re: crystal ligand-protein complex (Tsjerk
> Wassenaar)
>    8. RE: Fatal Error: UNK (Dallas B. Warren)
>    9. Distorted bonds (Chris Gaughan)
> 
> 
>
----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 26 Sep 2005 18:01:55 +0530 (IST)
> From: "Amol D. Atre" <ssb4 at udct.org>
> Subject: [gmx-users] Fatal Error: UNK
> To: gmx-users at gromacs.org
> Message-ID:
> <36037.192.16.6.198.1127737915.squirrel at email.uict>
> Content-Type: text/plain;charset=iso-8859-1
> 
> Hello all,
> 
> I generated pdb file using Export to pdb function
> available in Ghemical.
> When I ran pdb2gmx I get the following error,
> 
> Fatal error: Residue 'UNK' not found in residue
> topology database
> 
> Command line: pdb2gmx -f molecule.pdb -o
> molecule.gro -p molecule.top
> 
> Please help.
> 
> Waiting for reply.
> 
> Regards,
> Amol D. Atre.
> Lab No.A002,
> Chemical Engineering Department,
> Mumbai University Institute of Chemical Technology,
> Matunga(E), Mumbai-400019.
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 26 Sep 2005 14:53:51 +0200 (CEST)
> From: Jozef Hritz <hritz at seneca.science.upjs.sk>
> Subject: [gmx-users] Re: gmx-users Digest, Vol 17,
> Issue 63
> To: gmx-users at gromacs.org
> Message-ID:
> 
>
<Pine.LNX.4.10.10509261453430.5457-100000 at seneca.science.upjs.sk>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
> 
> 
> 
> 
>
==================================================================
>  Jozef Hritz                     |  e-mail:
> hritz at seneca.science.upjs.sk
>  Dept. of Biophysics, PF-UPJS    |  fax:   
> 00421-55-6222124
>  Jesenna 5                       |  phone: 
> 00421-55-6221926, kl.49
>  041 54 Kosice                   |  home page:
>  Slovakia                        |   
> http://bioflab.upjs.sk/~hritz
> 
>
==================================================================
> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Mon, 26 Sep 2005 15:06:27 +0200 (CEST)
> From: Jozef Hritz <hritz at seneca.science.upjs.sk>
> Subject: [gmx-users] second line in rtp
> To: gmx-users at gromacs.org
> Message-ID:
> 
>
<Pine.LNX.4.10.10509261455301.5457-100000 at seneca.science.upjs.sk>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
> 
> Hi,
> 
> Up to version ffG43a2, there are 8 parameters in the
> second line of .rtp
> file. 
> [ bondedtypes ]
> ; Col 1: Type of bond
> ; Col 2: Type of angles
> ; Col 3: Type of proper dihedrals
> ; Col 4: Type of improper dihedrals
> ; Col 5: Generate all dihedrals if 1, only heavy
> atoms of 0.
> ; Col 6: Number of excluded neighbors for nonbonded
> interactions
> ; Col 7: Generate 1,4 interactions between pairs of
> hydrogens if 1
> ; Col 8: Remove propers over the same bond as an
> improper if it is 1
> ; bonds  angles  dihedrals  impropers all_dihedrals
> nrexcl HH14 RemoveDih
>      2       2          1          2        0       
>  3      0     1
> 
> However in the higher versions (e.g. ffG43a3.rtp)
> there are only 4
> parameters. Does it mean that values
> all_dihedrals=0
> nrexcl=3
> HH14=0
> RemoveDih=1
> 
> are put there by default?
> 
> Thanks
> Jozef
> 
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Mon, 26 Sep 2005 14:53:58 +0200
> From: MGi? <magiofer at gmail.com>
> Subject: Re: [gmx-users] Fatal Error: UNK
> To: ssb4 at udct.org,	Discussion list for GROMACS users
> 	<gmx-users at gromacs.org>
> Message-ID:
> <e6acc8ab05092605537658799 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> what kind of molecule are you working on? GROMACS
> force field does not
> include many different types of molecules apart from
> protein and nucleic
> acids. it seems that the molecule you have created
> is of an unknown type. if
> it is the case, you have to build a topology file on
> purpose.
> yours,
> Magiofer
> 
> On 9/26/05, Amol D. Atre <ssb4 at udct.org> wrote:
> >
> > Hello all,
> >
> > I generated pdb file using Export to pdb function
> available in Ghemical.
> > When I ran pdb2gmx I get the following error,
> >
> > Fatal error: Residue 'UNK' not found in residue
> topology database
> >
> > Command line: pdb2gmx -f molecule.pdb -o
> molecule.gro -p molecule.top
> >
> > Please help.
> >
> > Waiting for reply.
> >
> > Regards,
> > Amol D. Atre.
> > Lab No.A002,
> > Chemical Engineering Department,
> > Mumbai University Institute of Chemical
> Technology,
> > Matunga(E), Mumbai-400019.
> >
> 
=== message truncated ===



	
		
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