Mgio you were right, my topology file is empty. However I
could
generate the .gro file (that seems to be ok) with editconf. Well now
the problem is how to have the topology file... Residue 38
C is the
problem, but I also think it should not exist! As I am new as Gromacs
user I donīt know what I have to do to correct my topology file... I
tried the -inter and -ter options as Dodd wrote, but it was not
clear for me how to use them correctly, so it did not work.
Do I have to specify none only fot the C residue? More
information about this would be great, thank you very much in advance!<br> Fernando Mattio<br><div><span class="gmail_quote">2005/9/28, Alan Dodd <<a href="mailto:anoddlad@yahoo.com">anoddlad@yahoo.com</a>>:</span>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Residue 38 is probably a C-terminal amidation, and<br>should not have a C in it anyways. I had the same
<br>problem with my peptide... use the option -inter, or<br>-ter (specifying none at the interactive prompt for<br>the c-terminus), to see if you can persuade gromacs to<br>realise it's just a terminal residue. If that doesn't
<br>work, you may need to tinker with the terminus files<br>in share/top. Make sure you examine any .gro file<br>produced to be sure there's still the amidation there.<br><br>--- MGiō <<a href="mailto:magiofer@gmail.com">
magiofer@gmail.com</a>> wrote:<br><br>> it is possible that residue 38 is not complete in<br>> your structure, in<br>> particular it has no C atom in its backbone, so the<br>> tompology cannot be<br>> written for that atom, have you checked if the .top
<br>> file is complete?<br>> the simplest thing you can try to obtain the<br>> correspondent .gro file from a<br>> .pdb file is using editconf<br>><br>> editconf -f input.pdb -o output.gro<br>><br>> but I suspect thet, il the structure is not complete
<br>> editconf will stop<br>> anyway.<br>> good luck!<br>><br>> Magiofer<br>><br>><br>><br>> On 9/28/05, Fernando Mattio <<a href="mailto:mattiofer@gmail.com">mattiofer@gmail.com</a>><br>> wrote:
<br>> ><br>> > Dear Gromacs users,<br>> ><br>> > I started from a file 1WFA.pdb, and after using<br>> the command<br>> > pdb2gmx -f 1WFA.pdb -p WFA.top -o WFA.gro<br>> > I expected to have the file
WFA.gro<br>> > However, this fatal error message appears: Fatal<br>> error: atom C not found<br>> > in residue 38NH2 while combining tdb and rtp<br>> > Probably for this reason the file WFA.gro was not
<br>> created! But the WFA.top and<br>> > the WFA_A.itp were created!<br>> > I really would like to create this .gro file, once<br>> I read this kind of<br>> > file is better than the .pdb ... I donīt think the
<br>> command is wrong... and I<br>> > started from a pdb file already created! So what<br>> is the problem? How can I<br>> > correct this?<br>> > So please, if anyone knows what should I do to<br>
> have this .gro file it<br>> > would be nice.<br>> ><br>> > Thank you very much in advance,<br>> > Fernando.<br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list
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