<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><br>
<div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div id="yiv1060757216"><div><div style="color:#000;background-color:#fff;font-family:arial, helvetica, sans-serif;font-size:12pt;"><div><span>Thanks for your suggestions.<br><br></span></div><div>The total charge is zero in real but what I got through swissparam is as below:</div><div>[ atoms ] <br>; nr type resnr resid atom cgnr charge mass <br> 1 C=O 1 LIG C 1 0.4500 12.0110 <br> 2 O=C 1 LIG O 2 -0.5700 15.9994 <br> 3 HCMM 1 LIG H1 3 0.0600 1.0079 <br> 4 HCMM 1 LIG H2 4 0.0600 1.0079 <br></div><div>So I entered as I showed
you.</div><div><br></div><div>In addition how can I add the proton on it? Editing the C to CT1 is right? or I have to add any charge here?</div><div><br></div><div>Formyl is connected to valine in the peptide
sequence in this .pdb file. Now, what about adding this line ?: <br></div><div>[ dihedrals ]<br> O C +N CA <br></div><div><br></div><div>Cheers,</div><div>Shima<br></div> <div style="font-family:arial, helvetica, sans-serif;font-size:12pt;"> <div style="font-family:times new roman, new york, times, serif;font-size:12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br> <b><span style="font-weight:bold;">To:</span></b> Shima Arasteh <shima_arasteh2001@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight:bold;">Sent:</span></b> Saturday, May 12, 2012 10:07 PM<br> <b><span style="font-weight:bold;">Subject:</span></b> Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs<br> </font> </div> <br>
<br><br>On 5/12/12 1:32 PM, Shima Arasteh wrote:<br>> Dear gmx users,<br>><br>> I want to simulate a peptide in water. The peptide has a formyl residue as the<br>> N-terminus. I got the parameters of it and then add it to the .rtp file of<br>> charmm36.ff as below:<br>><br>> [ For ]<br>> [ atoms ]<br>> ; name type charge chargegroup<br>> C C 0.4500 0<br>> O O -0.5700 0<br>> [ bonds ]<br>> ; ai aj fu b0 kb, b0 kb<br>> 1 2 1 0.12220 779866.6 0.12220 779866.6<br>><br>> [ pairs ]<br>> ; ai aj fu<br>><br>> [ angles ]<br>> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub<br>> 2 1 3 1 123.4390 403.48 123.4390 403.48<br>> 2 1 4 1 123.4390 403.48 123.4390 403.48<br>><br>> [ dihedrals ]<br>> ; ai aj ak al fu phi0 kphi mult phi0 kphi mult<br>><br>> But when I do what I described, I face this fatal error:<br>> Fatal error:<br>> No atoms found in .rtp file in residue
pairs<br>><br>> Would you help me with this problem? Did I add the formyl in a wrong way?<br>><br><br>Your [pairs] directive is empty, hence the error. Your [dihedrals] directive <br>will also produce the same error. There are no possible pairs in a unit <br>containing so few atoms, so you don't even need this. You may need to define <br>dihedrals, however, but they also depend upon the next residue.<br><br>You also have several other mistakes:<br><br>1. A formyl group has a proton on it; yours has none<br>2. Your net charge on the formyl group is not zero, though this may or may not <br>be a consequence of point #1<br>3. There is no connectivity information for linking to the next residue, which <br>will mean the formyl group will not be chemically bonded. This also affects <br>your dihedrals.<br><br>-Justin<br><br>-- <br>========================================<br><br>Justin A. Lemkul, Ph.D.<br>Department of
Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a rel="nofollow" target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br><br>========================================<br><br><br> </div> </div> </div></div></div><br><br> </div> </div> </div></body></html>