<br>
Hi Sven,<br>
<br>
Besides, you're better off with a topology (.itp) for a single glycine
which you #include in the .top file, rather than running the box with
200 glycines through pdb2gmx. The program would fail to notice that the
molecules are not attached to each other, unless you give them all
unique chain identifiers :p or have a TER statement after every single
glycine. But in that case pdb2gmx will generate 200 .itp files for you,
which may also not reflect your needs. Check the topology file section
in the manual (chapter 5).<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 10/24/05, <b class="gmail_sendername">Erik Lindahl</b> <<a href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><blockquote type="cite"></blockquote><div><font color="#0000dd">Hi,</font></div><span class="q"><br><blockquote type="cite"><div style="margin: 0px; min-height: 14px;"></div><div style="margin: 0px;">Fatal
error: Atom H1 in risidue GLY 2 not found in rtp entry with 7 atoms
while sorting atoms. maybe different protonation state. remove this
hydrogen or choose a different protonation state. Option -ignh will
ignore all hydrogens in the input.</div><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px;">I used force field # 3. Could you please explain to me how can I solve this?</div></blockquote></span>
</div><div><font color="#0000dd"><br></font></div><div>GROMOS96
45a3 is a united-atom force field, i.e. nonpolar hydrogens are merged
with the carbons. Use the option "-ignh" to ignore the hydrogens in the
input coordinate file, or choose an all-atom force field like OPLS-AA/L
instead.</div><div><span class="e" id="q_10723e3f0add5737_3"><div><br></div><div>Cheers,</div><div><br></div><div>Erik</div><br><div> <span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">
<div>-----------------------------------------------------------</div><div>Erik Lindahl <<a href="mailto:lindahl@sbc.su.se" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">lindahl@sbc.su.se</a>>
</div><div>Assistant Professor, Stockholm Bioinformatics Center</div><div>Stockholm University, SE 106 91 Stockholm</div><div>Phone: +46 8 5537 8564 Fax: +46 8 5537 8214</div><div><br></div><div><br></div><br></span>
</div><br>
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gmx-users-request@gromacs.org</a>.<br><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry
<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>