<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Thank you so much.</span></div><div><span>Shima</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 size="2" face="Arial"> <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, April 14, 2012 9:28 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Define a new residue in oplsaa<br> </font> </div> <br>
<br><br>Shima Arasteh wrote:<br>> Dear Justin,<br>> Thank you so much.<br>> Are these changes beneficial for other force fields too?<br>> <br><br>All force fields have to be modified individually and parameters reassigned based on the underlying methodology for parameterization. Thus, the changes you make in OPLS-AA have no use in other force fields. The same strategy is used, of course (per the link on adding residues to a force field), but the parameters that are added will be different in each case.<br><br>-Justin<br><br>> Cheers,<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:* Shima Arasteh <<a ymailto="mailto:shima_arasteh2001@yahoo.com" href="mailto:shima_arasteh2001@yahoo.com">shima_arasteh2001@yahoo.com</a>>; 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, April 14, 2012 9:19 PM<br>> *Subject:* Re: [gmx-users] Define a new residue in oplsaa<br>> <br>> <br>> <br>> Shima Arasteh wrote:<br>> > Dear GROMACS users,<br>> > I wanna add add a FOR residue containing atom C and O. In oplsaa force field, the most similar residue to formyl (FOR) is ACE.<br>> > How I can change the ACE in .rtp file in oplsaa ff to define FOR residue as a new residue?<br>> > I did like this, Is it correct?<br>> ><br>> <br>> No. See below.<br>> <br>> > [ ACE ]<br>> > [ atoms ]<br>> > CH3 opls_135 -0.180 1<br>> > HH31 opls_140 0.060 1<br>>
> HH32 opls_140 0.060 1<br>> > HH33 opls_140 0.060 1<br>> > C opls_235 0.500 2<br>> > O opls_236 -0.500 2<br>> > [ bonds ]<br>> > CH3 HH31<br>> > CH3 HH32<br>> > CH3 HH33<br>> > CH3 C<br>> > C O<br>> > [ impropers ]<br>> > CH3 +N C O improper_O_C_X_Y<br>> ><br>> > [ FOR ]<br>> > [ atoms ]<br>> > HH31 opls_140 0.060 1<br>> >
HH32 opls_140 0.060 1<br>> > HH33 opls_140 0.060 1<br>> <br>> A formyl group has only one H atom, since it is an aldehyde.<br>> <br>> > C opls_235 0.500 2<br>> > O opls_236 -0.500 2<br>> <br>> The charges here for C, H, and O will likely have to be recalculated. See:<br>> <br>> http://www.gromacs.org/Documentation/How-tos/Parameterization<br>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field<br>> <br>> > [ bonds ]<br>> > C O<br>> <br>> You need a C-H bond as well.<br>> <br>> > [ impropers ]<br>> > CH3 +N C O
improper_O_C_X_Y<br>> ><br>> <br>> There is no CH3 in a formyl group.<br>> <br>> -Justin<br>> <br>> -- ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a> <http://vt.edu> | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> <br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<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"
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