<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:14pt"><div><font size="3"><span>Thanks for your suggestions.</span></font></div><div><font size="3"><span>Now, I think that it's better to add the N atom of next residue to the .pdb file and then add hydrogen atoms to its .mol2 format. Because when I open formyl.pdb in chimera software and add hydrogens to it, it becomes an </span>formaldehyde and then I get the a wrong parameters in .itp file by using SwissParam. So I didn't remove the N atom which connects to the C of formyl. Now I got this .itp file:</font></div><div><font size="3"> <br></font></div><div><font size="3">; nr type resnr resid atom cgnr charge mass <br> 1 CR 1 LIG C 1 0.5500 12.0110 <br> 2 OR 1 LIG O 2 -0.6800
15.9994 <br> 3 HCMM 1 LIG H4 3 0.0000 1.0079 <br> 4 HCMM 1 LIG H6 4 0.0000 1.0079 <br> 5 HOR 1 LIG H8 5 0.4000 1.0079 <br> 6 NR 1 LIG N 6 -0.9900 14.0067 <br> 7 HNR 1 LIG H2 7 0.3600 1.0079 <br> 8 HNR 1 LIG H1 8 0.3600 1.0079 <br></font></div><div><font size="3"><br></font></div><div><font size="3">Would this file work probably? I mean can I get the correct parameters?</font></div><div><font size="3"><br></font></div><div><font size="3">The .rtp file which I arranged, is as below:</font></div><div><font size="3">[ For ]<br> [
atoms ]<br>; name type charge chargegroup<br> C CTL1 0.5500 0<br> O O -0.6800 0<br> H HC 0.1300 0<br> [angles ]<br> ai aj ak <br> O C +N <br> O C H</font></div><div><font size="3"> H C +N<br><br> [ bonds
]<br> C O <br> C +N<br> C H<br> <br> [ dihedrals ]<br> O C +N +CA <br> H C +N +H</font></div><div><font size="3"> H C +N +H</font></div><div><font size="3"><br></font></div><div><font size="3">Would it be correct? I got the charge of H atom by assuming the total charge of formyl is zero.</font></div><div><font size="3"><br></font></div><div><font size="3"><br></font></div><div><font size="3"><br></font></div><div><font size="3"><br></font></div><div><font size="3"><br></font></div><div><font size="3">Sincerely,<br>Shima</font><br></div> <div style="font-family: arial, helvetica, sans-serif;
font-size: 14pt;"> <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 9:40 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 12:42 PM, Shima Arasteh wrote:<br>> OK, so I entered the H atom corresponding to the structure and then changed the<br>> file as below,<br>><br>> [ 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<br>><br><br>I find it highly unlikely that a zero charge should be assigned to this proton. <br> The .itp file you posted before from SwissParam was for formaldehyde, which <br>suggests to me you haven't properly parameterized the species you're looking for <br>and now you're trying to hack something together. Don't try to do that; your <br>parameters will be junk. Parameterize the right species once and proceed from <br>there.<br><br>> [angles ]<br>> ai aj ak<br>> O C +N<br>> O C H<br>><br>> [ bonds ]<br>> C O<br>> C +N<br>> C H<br>><br>> [ dihedrals ]<br>> O C +N +CA<br>> H C +N
+H<br>><br><br>There are other possible dihedrals here.<br><br>-Justin<br><br>><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:* Sunday, May 13, 2012 8:36 PM<br>> *Subject:* Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs<br>><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> <mailto:<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>> <mailto:<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<br>> 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<br>> 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>> <mailto:<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"
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href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>>.<br>> > Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>> ><br>> ><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 | (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 href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a><br>> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a
href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>><br>><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 | (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><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 href="http://www.gromacs.org/Support/Mailing_Lists/Search"
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