True. I checked the files and found that CO was not described in any of
them and I did take care of the replacement ot A with a blank.<br>
Well in this case do I have any alternatives?<br>
Like other compatible force fields or modification of the existing one.<br>
<br>
Annie Albin. <br>
<br><br><div><span class="gmail_quote">On 3/31/06, <b class="gmail_sendername">MGiò</b> <<a href="mailto:magiofer@gmail.com">magiofer@gmail.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;">
<div style="direction: ltr;">That means that the CO ion type is not
described by the forcefield you are using, check the .rtp file of your
force field or the ions.itp file in the gromacs/top directory. anyhow
be careful not to make any confusion between the chain identifier,
which is a 1 character id, and the residue name. Are you sure you're
not shifting the columns of your pdb when deleting the chain identifier
(chain A shoud be replaced by a blank)?
</div><div style="direction: ltr;"><span class="e" id="q_10a505c3215638a7_1"><br><br>MG<br><br><div><span class="gmail_quote">On 3/31/06, <b class="gmail_sendername">Annie Albin</b> <<a href="mailto:anniealbin@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
anniealbin@gmail.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;">
<div style="direction: ltr;">Well thank you.Yes I did find a region in which chain identifier 'A'
was repeating, this corresponded to the HETATM CO, so i tried removing
the chain identifier in one case and in another one I tried shifting it
to the correspoding chain, but in both cases i got the following error <br>
"Fatal error:<br>
Residue 'CO' not found in residue topology database".<br>
Will be glad to hear any suggestions.<br>
Is there any other way in GROMACS to handle proteins with metal ions in it?<br>
<br>
Thank You,<br></div><div style="direction: ltr;"><span>
Annie Albin.</span></div><div style="direction: ltr;"><span><br>
<br>
<br><br><div><span class="gmail_quote">On 3/31/06, <b class="gmail_sendername">MGiò</b> <<a href="mailto:magiofer@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">magiofer@gmail.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;">
<div style="direction: ltr;">Hi!<br>it seems that pdb2gmx has detected
an interruption in your chain A numbering, are you sure that there are
none? or else are you sure that you're not using the same chain id for
more than one chain? for example for two different monomers?
<br>hope it helps,<br>MG<br><br><div></div><div style="direction: ltr;"><span><span class="gmail_quote">On 3/31/06, <b class="gmail_sendername">Annie Albin</b> <<a href="mailto:anniealbin@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
anniealbin@gmail.com</a>> wrote:</span></span></div><div style="direction: ltr;"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"></blockquote>
</div><div style="direction: ltr;"><span>
<div style="direction: ltr;">Dear all,<br>
<br>
I faced a problem in the pdb2gmx step as i got this following error message,<br>
"Fatal error:<br>
Chain identifier 'A' was used in two non-sequential blocks (residue 908, atom 7013)"<br>
<br>
As I'm pretty new to this field. I'm finding it difficult to troubleshoot. Any suggestions would be of great help.<br>
Thank you,<br></div><div style="direction: ltr;"><span>
Annie Albin.<br>
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