Thank u so much Mark. Is there any parameterization to mention forcefield and co ordinates in aminoacids.rtp in the fields of atoms, bonds (like C1 opls_195 +0.365 1 ). I checked the co ordinates in .pdb and .rtp files. Both are not the same. <br>
<br><br><br><div class="gmail_quote">On Fri, Mar 9, 2012 at 11:56 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div><div class="h5">
On 9/03/2012 4:56 PM, pragna lakshmi wrote:
<blockquote type="cite">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" target="_blank">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>
</blockquote>
</div>
</blockquote>
<br></div></div>
Your coordinate file doesn't match your .rtp entry regarding atom
O5.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
</font></span></div>
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<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>
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