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On 19/01/2012 3:17 PM, bharat gupta wrote:
<blockquote
cite="mid:CAAh+zSVdQ67ZcGA_KxeuRxq-CN0gAaCM1tjO-oxADSf2xqUfkA@mail.gmail.com"
type="cite">No. I am not trying to crosslink the chromophore with
nay residue but I have linked it with neighboring Valine(68) and
Leucine(64) by specifying the bonds in specbond.dat file. <br>
</blockquote>
<br>
You still have to go and look at residue 51 and see what is going
on. The problem can be independent of the chromophore, as Peter was
suggesting.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAAh+zSVdQ67ZcGA_KxeuRxq-CN0gAaCM1tjO-oxADSf2xqUfkA@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Thu, Jan 19, 2012 at 12:09 PM, Peter
C. Lai <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Are you
crosslinking the chromophore to an atom in residue 51?<br>
<br>
Can you generate a correct topology without the chromophore as
a check?<br>
<div>
<div class="h5"><br>
On 2012-01-19 11:50:37AM +0900, bharat gupta wrote:<br>
> Hi,<br>
><br>
> I have been trying to attach the chromophore of GFP
in charmm ff parameter<br>
> files. The parameters have been obtained from a
published article. After<br>
> making the changes as per the documentation (<br>
> <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field"
target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a>)<br>
> , I am getting following error :-<br>
><br>
> Atom CG is used in an interaction of type atom in the
topology<br>
> database, but an atom of that name was not found in
residue<br>
> number 51<br>
><br>
> The chromophore residue number is 66, I don't
understand why there is an<br>
> error for residue 51 . Please help me in rectifying
this error ..<br>
><br>
> Regards<br>
><br>
> --<br>
> Bharat<br>
<br>
</div>
</div>
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<br>
--<br>
==================================================================<br>
Peter C. Lai | University of
Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br>
<a moz-do-not-send="true" href="mailto:pcl@uab.edu">pcl@uab.edu</a>
| Birmingham AL 35294-4461<br>
(205) 690-0808 |<br>
==================================================================<br>
<br>
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</font></span></blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343
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