Hi Jack,<br><br><div class="gmail_quote">On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz <span dir="ltr"><<a href="mailto:js@drugdiscoveryathome.com">js@drugdiscoveryathome.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>Problem Solved.</div>
<div> </div>
<div>I replaced HETATM with ATOM, I fixed BOTH N-terminal and C-terminal. I kept TER and END. Removed all CONECT. Renamed the CYS to CYS2. No other non-AminoAcid residues were present. Most of this is described by the FFAmber site</div>
<div><a href="http://chemistry.csulb.edu/ffamber/" target="_blank">http://chemistry.csulb.edu/ffamber/</a></div>
<div> </div></blockquote><div><br>Gromacs doesn't distinguish between ATOM and HETATM entries.<br>Gromacs does not read CONECT records.<br>Now the 'TER' recoord... That makes a difference. <br><br>Cheers,<br>
<br>Tsjerk<br></div></div><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br><br>Computational Chemist<br>Medicinal Chemist<br>Neuropharmacologist<br><br>