<DIV><FONT face="times new roman" size=4>Hi Mark,</FONT></DIV> <DIV><FONT face="times new roman" size=4></FONT> </DIV> <DIV><FONT face="times new roman"><FONT size=4>Thank you for your valuable suggestion.I did go through the manual, but I want to confirm if I need to add the atom CA in the ffoplsaa.rtp file, and if so I am not sure what the appropiate <SPAN style="FONT-FAMILY: 'Courier New'"> Type of angles, Type of proper dihedrals, Type of improper dihedrals I have to enter.</SPAN></FONT></FONT></DIV> <DIV><FONT face="times new roman" size=4><SPAN style="FONT-FAMILY: 'Courier New'">If I choose the force field with option 0 then it gives me an error saying residue AIB not found in residue topology.</SPAN></FONT></DIV> <DIV><FONT face="times new roman" size=4><SPAN style="FONT-FAMILY: 'Courier New'"></SPAN></FONT> </DIV> <DIV><FONT face="times new roman" size=4><SPAN style="FONT-FAMILY: 'Courier New'">Any help would be highly
appreciated.</SPAN></FONT></DIV> <DIV><FONT face="times new roman" size=4><SPAN style="FONT-FAMILY: 'Courier New'">Thanks,</SPAN></FONT></DIV> <DIV><FONT face="times new roman" size=4><SPAN style="FONT-FAMILY: 'Courier New'">Aj</SPAN></FONT><BR><BR><B><I>Mark Abraham <Mark.Abraham@anu.edu.au></I></B> wrote:</DIV> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">ASHWINI JAYAPRAKASH wrote:<BR>> Hi,<BR>> <BR>> I am a new gromacs user and have problems creating a topology file using <BR>> the pdb2gmx command for simulating a six helix bundled alamethecin in <BR>> lipid bilayer.<BR>> when I use the command :<BR>> pdb2gmx -f almN6start -o almN6start.gro -p almN6start.top<BR>> <BR>> I get the error :<BR>> <BR>> Program pdb2gmx, VERSION 3.3.1<BR>> Source code file: pdb2gmx.c, line: 393<BR>> Fatal error:<BR>> Atom CA in residue ACE 1 not found in rtp entry with 6 atoms<BR>>
while sorting atoms<BR><BR>This means what it says. pdb2gmx is finding a CA atom in an ACE residue <BR>in your coordinate file that it can't reconcile with the .rtp entry for <BR>ACE for the force field you're using. If this doesn't make any sense, <BR>you should read chapter five of the manual thoroughly. Probably the <BR>first four chapters are also worth reading too.<BR></BLOCKQUOTE><p> 
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