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On 21/11/2011 9:28 PM, archana sonawani wrote:
<blockquote
cite="mid:CAFV47mgL7bOXTpi49fW_VO87q2RNWg3Pa1g1-W1bX_DmmLECuw@mail.gmail.com"
type="cite">Dear Sir/madam,
<div><br>
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<p class="MsoNormal"><span class="apple-style-span"><span
style="mso-bidi-font-size:12.0pt;font-family:"Arial","sans-serif";color:#333333;background:white"
lang="EN-US">I have a ligand molecule for which I
generated the topology
file using Prodrg software. As the charges and groupings
provided by Prodrg are
not much reliable. I need to assign correct charges and
groupings for my
ligand. I had referred the article "Practical
considerations for building GROMOS-compatible
small-molecule topologies". I could assign charges and
groupings for most of the molecule except for the
heterocyclic structures and sulfur atom in ring. Please
help me out...Thanks in advance..</span></span></p>
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</blockquote>
<br>
Welcome to the jungle. :-) Paramterization is an expert topic for a
reason. You should search the literature to find what approaches
have been used for such heteroatoms and see what might be applicable
to your case. Regardless, you will need to demonstrate that your
parameters do a decent job on some known experimental data before
they can be supposed to have value for a computational study.<br>
<br>
Mark<br>
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