Hi Guillem,<div><br></div><div>Many thanks for your clarification. I was lazy to find out and remember why psc0 was not ported to GMX by ffAmber previously and it was exactly because what you've said. </div><div><br></div>
<div>And because I was not confident enough, I didn't implement that for acpypi, which I believe does better than amb2gmx in general, so I would be glad if you could take a look at it and if you could let me know which modifications you did to amb2gmx.<br>
<br></div><div>I am taking plunge in this problem again and I'll try to come out with a solution based in what you suggest.</div><div><br></div><div>Cheers,</div><div><br></div><div>Alan</div><div><br><div class="gmail_quote">
On Fri, Apr 9, 2010 at 00:53, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div id=":3tt" class="ii gt">Right, the only dihedral angles that do not allow an exact translation to<br>
RB because of the phase are the ones involving the new parametrization for<br>
nucleic acids. Namely, it corrects the alpha/gamma transitions to get the<br>
populations of states right, thus avoiding the loss of helicity on the<br>
long run. For proteins, there's no difference at all, so you can use<br>
ffamber.<br>
<br>
I've used the combined approach you mention without problems. The only<br>
thing is that I do not use pdb2gmx. Rather I use amber's tools<br>
(leap+libraries, all free in ambertools) to get a topology, and then I use<br>
a slightly modified version of <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> script to get a gromacs<br>
topology. I only convert the new parmbsc0 dihedrals to type 1 if the phase<br>
does not allow a direct conversion to RB form. Typically you have three<br>
entries for the same dihedral, this is no problem at the itp level, grompp<br>
captures them all. With this approach I reproduced a torsional scan of<br>
parmbsc0 from amber md tool using gromacs, so I feel confident about it.<br>
<br>
Another option is to use the ffamber parameters and change the itp file<br>
including the new ones.<br>
<br>
I should also mention that I had problems importing the new dihedrals<br>
using pdb2gmx. IIRC, pdb2gmx will only use one definition for dihedral if<br>
type 1 or 3 is used. There was a new dihedral type that could be used in<br>
the development versions, but... for a reason it did not work out for me,<br>
don't recall exactly why. It could well be that it would have worked with<br>
more patience from my side.<br>
<br>
Hope this helped, somehow. You were on the right direction anyway.<br>
<br>
best,<br>
<br>
Guillem<br></div></blockquote></div><br><br clear="all"><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
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