Thanks chris,<br>
it worked..:)<br>
thanks others for your inputs..:)<br><br><div><span class="gmail_quote">On 12/14/05, <b class="gmail_sendername">Chris Gaughan</b> <<a href="mailto:clgaughan68@yahoo.com">clgaughan68@yahoo.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Can you give each chain different lables using -label<br>in editconf? That may well be the problem. Also,<br>gromacs doesn't seem to recognize Ter cards for some<br>reason. I had the same problem when simulating<br>dimerization of two peptide chains. It treated them as
<br>one single unit. I just used the -label option for<br>each pdb and then concatenated.<br><br>--- Pradeep Kota <<a href="mailto:kotanmd@gmail.com">kotanmd@gmail.com</a>> wrote:<br><br>> thanks Mr.Larsson..<br>
> but i checked the pdb file for such errors and<br>> couldnt find any. there are<br>> four chains in my pdb file. and each chain is named<br>> separately and all<br>> chains are separated by ter tags properly. is there
<br>> any other possibility of<br>> this error?<br>> thanks again..<br>> reg.<br>> tand<br>><br>><br>> On 12/14/05, Per Larsson <<a href="mailto:per.larsson@sbc.su.se">per.larsson@sbc.su.se</a>>
<br>> wrote:<br>> ><br>> > Check your pdb-file using a text editor of some<br>> sort.<br>> > Probably you have the same chainID for some<br>> residues with another (or<br>> > possibly none) chain ID in between. All residues
<br>> belonging to the same<br>> > chain need to have the same chain identifier.<br>> ><br>> > Regards<br>> > /Per<br>> ><br>> ><br>> > Pradeep Kota wrote:<br>> ><br>> > > hi
<br>> > > i'm new to gromacs<br>> > > pdb2gmx gives an error<br>> > > i have a two subunit protein<br>> > > pdb2gmx says<br>> > > fatal error : use of same chain marker A in non
<br>> sequential residues<br>> > > and it displays the atom number also.<br>> > > i checked the pdb file and the two domains are<br>> file and i visualised<br>> > > them using rasmol. wat do i do?
<br>> > > thanks for any help<br>> > > tand<br>> > ><br>> ><br>><br>>------------------------------------------------------------------------<br>> > ><br>> > >_______________________________________________
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