<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>All right.</span><span><br></span></div><div><span>Thank you</span></div><div><br><span></span></div><div><span>Sincerely,</span></div><div><span>Shima<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> Saturday, May 12, 2012 10:36 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 5/12/12 2:00 PM, Shima Arasteh wrote:<br>> <br>> The total charge is zero in real but what I got through swissparam is as below:<br>> [ 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>> So I entered as I showed you.<br>> <br><br>What you parameterized was formaldehyde, not a formyl adduct group. I believe I said before to make sure you were deriving parameters appropriately, which it appears you are not.<br><br>> In addition how can I add the proton on it? Editing the C to CT1 is right? or I<br>> have to add any charge here?<br>> <br><br>I don't understand what you're asking here.<br><br>The .rtp entry specifies the necessary atoms. In your case, for a formyl group, you need 3 atoms - C, H, and O. I suspect that this addition will
change the amino acid residue to which it is attached, in which case you are better off deriving a completely new amino acid residue, or at least verifying that your new addition does not affect the charges of the existing amino acid (unlikely). I recommended this before; please make sure to heed all available advice before plowing ahead and doing something that doesn't make sense. It wastes your time and the that of others who are seeking to help you.<br><br>> Formyl is connected to valine in the peptide sequence in this .pdb file. Now,<br>> what about adding this line ?:<br>> [ dihedrals ]<br>> O C +N CA<br>> <br><br>This is incorrect. The CA atom is part of valine, thus it is the next residue and must also be prefixed with a + sign, as in the case of N. Using - (minus) indicates the previous residue, + the next, and no sign is the present residue. The correct line is:<br><br>O C +N
+CA<br><br>-Justin<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>-- 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" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
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