[gmx-users] How to ask pdb2gmx to print all parameters in the itp file

[Mark James Abraham]

----- Original Message -----
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Date: Saturday, February 16, 2008 6:03 pm
Subject: Re: [gmx-users] How to ask pdb2gmx to print all parameters in the itp file
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi,
> 
> grompp allows you to write the (cpp) processed topology (-pp). Since
> many parameters are controlled using cpp #define statements, cpp has
> to be called to fill the values. pdb2gmx can't do that.

The OP wanted a tool to do more than #include, they also wanted something to perform mapping of interaction functions from atom numbers to atom types to parameters. The only straightforward way to do this is via grompp. Either use gmxdump on the .tpr file resulting from grompp and parse the output (remember that numbering now starts at zero, whereas in the .top it starts at 1), or write a new output module for grompp to do what you want it to do, or write a new program to parse the .tpr file, since you can re-use a lot of existing code from mdrun which has to do the same task.

Mark

> On Feb 15, 2008 6:46 PM, Alan Dodd <anoddlad at yahoo.com> wrote:
> > If you convert the tpr binary into a text file, it should have 
> every parameter in it I think?
> >
> >
> > ----- Original Message ----
> > From: LeeHui <emiemismile at hotmail.com>
> > To: gmx-users at gromacs.org
> > Sent: Friday, February 15, 2008 4:57:13 PM
> > Subject: [gmx-users] How to ask pdb2gmx to print all 
> parameters in the itp file
> >
> >
> > Dear all gmx users,
> >
> > I am converting the parameters in "itp" file into DL_POLY 
> format, and will be using it in my own version of DL-poly.
> > I was wondering if there is a way to ask pdb2gmx or some other 
> utilities in Gromacs to print all the parameters into itp, so I 
> don't have go to the database and find them out.
> >
> > eg. the default pdb2gmx generated itp have this format
> > [ angles ]
> > ;  ai    aj    ak 
> funct            c0            c1            c2            c3
> >     1    
> 2    3    1
> >     1    
> 2    4    1
> >     1    
> 2    5    1
> >     3    
> 2    4    1
> >
> > instead of leaving c0, c1.. blank, I want the exact values of 
> them printed .
> >
> > Is there a way to this in Gromacs ?
> >
> >
> > Thanks,
> >
> >
> > Hui
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> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
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