<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Again thanks for all your replies.</span></div><div><span>As I got through your advices, I found that the atoms contribute in making bonds and angles in a residue , or make dihedrals in a residue ( or with atoms in next ones) plus the charge of a the residue should be defined properly in .rtp files to define the new residue in aminoacid.rtp file of CHARMM36 force field.</span></div><div><span>So I arranged this lines to define formyl in .rtp file. And I got the topology. But there are some questions for me here:</span></div><div><br><span></span></div><div><span>1. How can I be sure the formyl which I defined is correct? Is getting the topology is enough to be sure of the correct output?<br></span></div><div><br><span></span></div><div><span>The .rtp file for formyl is as below:</span></div><div><span>[ For ]<br> [
atoms ]<br>; name type charge chargegroup<br> C CTL1 0.5700 0<br> O O -0.5700 0<br> [angles ]<br> ai aj ak <br> O C +N <br> [ bonds ]<br> C O <br> C +N<br> <br> [ dihedrals ]<br> O C +N +CA<br></span></div><div><br><span></span></div><div><span>2. There are lots of numbers in .itp file which
I got through the swissparam. But I think the charge of atoms may be useful in this file and also I can just find the atoms contribute in bonds and angles and.... . Am I right? Or I may get some other useful information which I can get through the files of swissparam?</span></div><div><br><span></span></div><div><span>Thanks in advance, and sorry for disturbing you friends.<br></span></div><div><span>Shima<br></span></div><div><span><br></span></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> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Saturday,
May 12, 2012 10:12 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 1:37 PM, Justin A. Lemkul wrote:<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 your<br>> dihedrals.<br>><br><br>Another that I just caught as I hit send:<br><br>4. In your [bonds] and [angles] directives, you use atom numbers - they should <br>be names<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 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>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search"
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