[gmx-users] Example file for DNA

[Tsjerk Wassenaar]

Hi,

I stripped the following from a script of mine. The original script
did some additional things before, involving first a conversion from
PDB to CNS format and later to GMX format. I rearranged it without
testing. You can try it and if you find that it doesn't do a proper
job, you can send me the before and after file.

Hope it helps (hope it works ;))

Tsjerk

###

#!/bin/bash

# RENAME RESIDUES
DNA_PDB2GMX='s/\(^.\{17\}\)DG  /\1DGUA/; s/\(^.\{17\}\)DA  /\1DADE/;
s/\(^.\{17\}\)DC  /\1DCYT/; s/\(^.\{17\}\)DT  /\1DTHY/'
RNA_PDB2GMX='s/\(^.\{17\}\) G  /\1 GUA/; s/\(^.\{17\}\) A  /\1 ADE/;
s/\(^.\{17\}\) C  /\1 CYT/; s/\(^.\{17\}\) U  /\1 URA/'

# RENAME ATOMS AND DELETHE HYDROGENS
NUCL_DELHYD="/^.\{13\}H.'/d; /^.\{13\}H7..THY/d; /^.\{12\}H5''/d"
THY_C72C5M='s/\(^.\{13\}C\)7 .THY/\15M.THY/'
NUCL_PDBS2GMX="$NUCL_DELHYD; $THY_C72C5M; s/\(^.\{12\}...\)'/\1\*/"

sed -e "{ $NUCL_PDB2GMX; $DNA_PDB2GMX; $RNA_PDB2GMX }" $1



On Sat, Oct 17, 2009 at 3:08 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> David Crosby wrote:
>>
>> Hello fellow GROMACS users!
>>
>> I've been having a heck of a time with the reformatting of a DNA molecule
>> into a GROMACS-compatible format.  I know that residues (bases) must be
>> renamed to DTHR, etc., though it would be endlessly helpful if someone
>> could
>> please send me an example pdb or gmx file I can use as reference.  Better
>> yet, if anyone has a nifty program that will reformat a nucleic acid model
>> into the GROMACS format, that would answer my prayers!  The duplex I'm
>> working with is only 21nt, so it's not insane to have to modify the file
>> by
>> hand...
>>
>
> A simple Perl script can make substitutions, or you can use a text editor
> like vi or a command like sed.  In about 4 commands, the whole file can be
> re-named.  In vi, for example:
>
> :1,$s/DT  /DTHY/g
>
> ...and all of your thymines are re-named (note the spacing is important).
>
> -Justin
>
>> Thanks in advance!
>> Dave Crosby
>>
>> University of California, Irvine
>> Dept of Pathology and Laboratory Medicine
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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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
F: +31-30-2537623