[gmx-users] want to remove H5T entry form HDB file / open terminal (P, O) for polymerization of i-motif

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 8 00:09:06 CEST 2011

raghav singh wrote:
> Hi Justin,
> Yeah I have to remove that H from the that position to make my P open to 
> contact with the O atom of the next unit.
> ..but if you make some precise suggestion that How can I remove that 
> entry.. because I have tried to remove the entry from .RTP and .HDB 
> files and in that case it starts giving me error that H5T is not 
> available in rtp and hdb entry.

You've not shown any evidence that anything you've tried should have even 
worked, for several reasons:

1. Your .pdb file contains a residue named DT, but your .rtp entries have never 
matched that name.  pdb2gmx will not match these entries if they do not have the 
same name.

2. The .rtp and .hdb entries you've shown previously specify that H5T should be 
there, or otherwise built on.  If you properly remove all references to H5T (and 
then consequently re-calculate the charges on the associated functional groups), 
then there is no way pdb2gmx will try to place the atom there.  It simply can't.

If you've gotten some error message, please copy and paste it rather than trying 
to interpret what you're seeing.

> I am just getting crazy with this thing... I am creating tons of DATA 
> but NOT even a single thing which I can say a CLOSE SOLUTION... the best 
> I found what I have posted. :(
> Need some serious help.. Passed the files to MY PROFESSOR :)

I understand that everyone has urgent problems to solve, including the people 
trying to give of their time to help you.  If you've gotten yourself in a bind, 
then I can't help that.  You've not yet posted any evidence of anything that 
might actually accomplish your goal.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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