<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>OK, so I entered the H atom corresponding to the structure and then changed the file as below,</span></div><div><br><span></span></div><div><span>[ For ]<br> [ atoms ]<br>; name type charge charge group<br> C CTL1 0.5700 0<br> O O -0.5700 0<br> H HC 0.00
0</span></div><div><span><br></span></div><div><span> [angles ]<br> ai aj ak <br> O C +N </span></div><div><span> O C H</span></div><div><span><br></span></div><div><span> [ bonds ]<br> C O <br> C +N<br> C H<br> <br> [ dihedrals ]<br> O C +N +CA <br> H C +N +H<br></span></div><div><br><span></span></div><div><span><br></span></div><div><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> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Sunday, May 13, 2012 8:36 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 5/13/12 11:43 AM, Shima Arasteh wrote:<br>> Again thanks for all your replies.<br>> As I got through your advices, I found that the atoms contribute in making bonds<br>> and angles in a residue , or make dihedrals in a residue ( or with atoms in next<br>> ones) plus the charge of a the residue should be defined properly in .rtp files<br>> to define the new residue in aminoacid.rtp file of CHARMM36 force field.<br>> So I arranged this lines to define formyl in .rtp file. And I got the topology.<br>> But there are some questions for me here:<br>><br>> 1. How can I be sure the formyl which I defined is correct? Is getting the<br>> topology is enough to be sure of the correct output?<br>><br><br>It is incorrect. As I said before, a formyl group is an aldehyde and has an H <br>atom attached to C, e.g. -CH(=O). At present, you are defining a -C=O group <br>with an incomplete carbon
valence.<br><br>http://en.wikipedia.org/wiki/Aldehyde<br><br>> The .rtp file for formyl is as below:<br>> [ 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>><br><br>Aside from the missing atom (and resulting missing bonds, angles, and dihedral), <br>the format of this entry is OK.<br><br>> 2. There are lots of numbers in .itp file which I got through the swissparam.<br>> But I think the charge of atoms may be useful in this file and also I can just<br>> find the atoms contribute in bonds and angles and.... . Am I right? Or I may get<br>> some other useful information which I can get through the files of swissparam?<br>><br><br>If the existing bonded parameters for each interaction type (in ffbonded.itp) <br>are sufficient for
defining these interactions, then you can omit the content of <br>the .itp file you've been using in the .rtp entry and rely on the force field to <br>look up those values. There may be some interactions that are not in agreement <br>(or do not exist), in which case you need to either define these parameters in <br>the .rtp entry itself or in ffbonded.itp so that they will be detected by grompp <br>later.<br><br>-Justin<br><br>> Thanks in advance, and sorry for disturbing you friends.<br>> Shima<br>><br>> --------------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Saturday, May 12, 2012 10:12 PM<br>> *Subject:* Re:
[gmx-users] Fatal error: No atoms found in .rtp file in residue pairs<br>><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]vt.edu <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><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> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a
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