Subject: Re: CCL:HELP WITH TINKER

From: Helmut Heller <[email-masked]>
Date: Sat, 30 Jan 1999 07:14:28 +0100

<nofill>040b73747265616d747970656481a203840163c4840373737381dadb81070781161684012584067f411b312d36 You wrote:
> I am trying to implement TINKER to run MD on biomolecules. I am unable 
> to do a minimization of a tripeptide in solution. the energy blows up.
> is there  an example file where i could look into? [it is a tripeptide 
> immersed in a 15A cube of tip3p waters]. the minimization in vaccum runs 
> fine. minimization/md of water alone runs fine too.
</nofill>

Most likely you were not carefull enough when you immersed the peptide
into the water cube and you ended up with vdW overlaps. Check the INITIAL
vdW energy! If it is high (several powers of 10) then your initial setup
is bad.

Helmut

---

<fontfamily><param>Helvetica</param>Servus, Helmut  (DH0MAD)             
___________ NeXT-mail welcome ________________

FAX: +49-8671</fontfamily><fontfamily><param>Symbol</param>-</fontfamily>
<fontfamily><param>Helvetica</param>881 665                      "
Knowledge must be gathered and cannot be given "

[email-masked]                                                    ZEN, one
of BLAKES7

Phone: +49-8671</fontfamily><fontfamily><param>Symbol</param>-
</fontfamily><fontfamily><param>Helvetica</param>881665                
---------------------------------------------------------------------------

Dr. Helmut Heller, Mühldorfer Str. 72, 84503 Altötting, GERMANY

</fontfamily>