[gmx-users] PRODRG again

[Ruben Martinez Buey]

Can you cut your molecule into smaller pieces and then join them?
As you only have ten residues more than permitted, another option is to 
use for example H instead acetate, etc... After creating the topology 
just change this.
Hope this help,
Cheers,
Ruben

Osmany Guirola Cruz wrote:

>I have a "drug" greater than 300 atoms what should I do to get the
>topology
>I don know if exist another program or server that do something similar 
>My drug have 310 atoms 
>Help please  :-(
>
>
>
>
>-----Original Message-----
>From: Daan van Aalten [mailto:vdava at davapc1.bioch.dundee.ac.uk] 
>Sent: Wednesday, May 19, 2004 9:58 AM
>To: Peter Zoon
>Cc: Discussion list for GROMACS users
>Subject: Re: [gmx-users] PRODRG
>
>
>
>Peter
>
>You are confusing topology with conformation. For each bond between a
>pair of atoms there is a choice of several hundreds of bond types, which
>are associated with a) specific force constants and b) specific
>equilibrium values (i.e. bond lengths). Same for bond angles. You can
>minimize coordinates, but the topology stays the same.
>
>Writing out a G96 FF topology is probably only a day's work if I can
>have a full day's use of a G96 FF guru for advice and testing - and of
>course everyone is busy!
>
>cheers
>
>Daan
>
>On Wed, 19 May 2004, Peter Zoon wrote:
>
>  
>
>>>The atom types aren't the problem but the manual conversion of 
>>>bonds/angles/dihedrals to G96 types. IMHO this may be intricate in 
>>>some cases. I guess it would be very nice to have a G96 topology 
>>>automatically generated by PRODRG, the GMX force field seems to be 
>>>considered rather outdated even by the Gromacs crew themselves.
>>>      
>>>
>>That doesn't matter right?
>>If you do a minimization (after you changed to the right atom-types), 
>>the system will just equilibrate and you will reach the right topology
>>    
>>
>
>  
>
>>automatically.
>>
>>Or am I making a reasoning error here?
>>
>>Peter
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>>    
>>
>
>
>########################################################################
>######
>Dr. Daan van Aalten                    Wellcome Trust RCD Fellow /
>Reader
>Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
>Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
>School of Life Sciences                E-mail: see WWW page
>Univ. of Dundee, Dundee DD1 5EH, UK    WWW:
>http://davapc1.bioch.dundee.ac.uk
>
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>  
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-- 
-----------------------------------------------
Ruben Martínez-Buey. PhD student.
Protein Function and Structure
Centro de Investigaciones Biológicas
Consejo Superior de Investigaciones Científicas
C/ Ramiro de Maeztu, 9
28040 Madrid (SPAIN)
phone:34-918373112 ext 4380
fax:  34-915360432
http://akilonia.cib.csic.es
-----------------------------------------------

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