I forgot to mention that i am using OPLS-AA/L all-atom force field.<br><br><div class="gmail_quote">On Fri, Mar 9, 2012 at 11:21 AM, pragna lakshmi <span dir="ltr"><<a href="mailto:pragnapcu@gmail.com">pragnapcu@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Gromacs Users,<br> I need to simulate a protein that has N-acetyl glucosamine (NAG). Since NAG residue is not present in residue topology file, first of all i added NAG parameters to aminoacids.rtp file. I am following this link <b><a href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a></b> <br>
<br>This is my aminoacids.rtp file for NAG.<br><br>[ NAG ] ; N-Acetylglucosamine<br><br>[ atoms ]<br> C1 opls_195 +0.365 1 <br> HC1 opls_196 +0.100 1<br> O1 opls_187 -0.700 1<br> HO1 opls_188 +0.435 1<br>
C5 opls_183 +0.170 1<br> HC5 opls_185 +0.030 1<br> O5 opls_180 -0.400 1<br> C2 opls_229 +0.140 2<br> HC2 opls_140 +0.060 2<br> N2 opls_238 -0.500 2<br> N15 opls_238 -0.500 2<br>
HN2 opls_241 +0.300 2<br> C3 opls_158 +0.205 3<br> HC3 opls_140 +0.060 3 <br> O3 opls_154 -0.683 3<br> O3H opls_155 +0.418 3<br> O2H opls_155 +0.418 3<br> C4 opls_158 +0.205 4<br>
HC4 opls_140 +0.060 4 <br> O4 opls_154 -0.683 4<br> OM opls_154 -0.683 4<br> O4H opls_155 +0.418 4<br> C6 opls_157 +0.145 5<br>HC61 opls_140 +0.060 5<br>HC62 opls_140 +0.060 5<br>
O6 opls_154 -0.683 5<br> O6H opls_155 +0.418 5<br> C7 opls_235 +0.500 6<br> O7 opls_236 -0.500 6<br> C8 opls_135 -0.180 7<br>HC81 opls_140 +0.060 7<br>HC82 opls_140 +0.060 7<br>
HC83 opls_140 +0.060 7<br> OR opls_154 -0.683 5<br> OW opls_154 -0.683 5<br><br>[ bonds ]<br> C1 HC1<br> C1 O1<br> C1 C2<br> C1 O5<br> O1 HO1<br> C2 HC2<br> C2 N2<br> C2 C3<br>
N2 HN2<br> N2 C7<br> C3 HC3<br> C3 O3<br> C3 C4<br> O3 HO3<br> C4 HC4<br> C4 O4<br> C4 C5<br> O4 HO4<br> C5 HC5<br> C5 O5<br> C5 C6<br> C6 HC61<br> C6 HC62<br> C6 O6<br>
O6 HO6<br> C7 O7<br> C7 C8<br> C8 HC81<br> C8 HC82<br> C8 HC83<br><br>Now i have got this error.<br><br>Fatal error:<br>Atom O5 not found in residue <a href="http://seq.nr" target="_blank">seq.nr</a>. 1 while adding atom<br>
<br>If any body knows solution for this, can you please reply this. If any error is there in aminoacids.rtp file, please mention it. I will change it accordingly. Any suggestion is appreciable. <br>
</blockquote></div><br><br clear="all"><br>-- <br><div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">T.Pragna Lakshmi,</span></div><div style="line-height:normal">
<span style="font-family:"Times New Roman","serif";font-size:12pt">Junior Scientist,</span></div><div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt"><span style="font-family:"Times New Roman","serif";font-size:12pt">Vision Research Center,</span></span></div>
<div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">Sankara Netralaya,</span></div><div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">Chennai,</span></div>
<div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">India.</span></div><div style="line-height:normal"><span style="font-family:"Times New Roman","serif";font-size:12pt">Pin: 600006.</span></div>
<div></div><br>