<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Hi Jianhui,</DIV>
<DIV> For your sugar part you can use PRODRG, which will convert coordinates for small molecules in <A title=Documentation/File_Formats/.pdb_File href="http://www.gromacs.org/Documentation/File_Formats/.pdb_File" rel=internal>PDB format</A> (or simple text structures) to the following topology formats: GROMOS, GROMACS and from literature if you can find out the parameters of ffG53a6 force field, then you can correct the charge, angle and dihedral values that you are collected from the PRODRG. Hope this will help you.</DIV>
<DIV>Regards...</DIV>
<DIV>Parichita...........</DIV>
<DIV><BR><BR> </DIV>
<DIV style="COLOR: rgb(0,0,127)">
<DIV><FONT face=arial>Parichita Mazumder <BR>Research Fellow <BR>C/O Dr. Chaitali Mukhopadhayay <BR>Department of Chemistry <BR>University of Calcutta <BR>92,A P C Road <BR>Kolkata-700009 <BR>India.</FONT></DIV></DIV><BR><BR>--- On <B>Wed, 18/8/10, Jianhui Tian <I><jianhuitian@gmail.com></I></B> wrote:<BR>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: Jianhui Tian <jianhuitian@gmail.com><BR>Subject: [gmx-users] carbohydrate parameters in ffG53a6<BR>To: gmx-users@gromacs.org<BR>Date: Wednesday, 18 August, 2010, 10:16 AM<BR><BR>
<DIV id=yiv305218139>Hi,<BR><BR>I want to do some simulations about carbohydrates and glycolipid. In the ffG53a6.rtp file, I just see limited parameters for carbohydrate, like monosaccharide Glucose, Mannose and Galactose. What parameters can be used for others like arabinose? Also, is there any parameters available in the Gromacs force field for glycolipid? <BR><BR>Jianhui <BR></DIV><BR>-----Inline Attachment Follows-----<BR><BR>
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