[gmx-users] naive question about the c-terminus
x.periole at rug.nl
Mon May 10 16:34:41 CEST 2010
On May 10, 2010, at 4:12 PM, abdullah ahmed wrote:
> Hello everyone!
> I have a naive question and I have been trying to find a solution
> myself, but I just don't understand what is wrong.
> When I run pdb2gmx with "-ter" on my molecule I get the following
> error message when I ask for a COOH to be made at the C terminus (I
> get no error when I ask for COO- ):
> Atom O2 not found in residue 22 while adding improper.
> However, My PDB file ends with:
> ATOM 282 C LEU B 44 -5.138 -16.681 4.219 1.00
> 0.00 B1 C
> ATOM 283 O1 LEU B 44 -4.407 -17.877 3.685 1.00
> 0.00 B1 O
> ATOM 284 O2 LEU B 44 -6.471 -16.388 3.597 1.00
> 0.00 B1 O
> TER 286 LEU B 44
> Therefore, the O2 atom is clearly there.
in residue 44!
Would you be working with a dimer ?
> I considered the idea that the error was because there is no
> Hydrogen at the end of the PDB file to make the H in COOH. So I used
> ZZ vega to add a hydrogen to O2. When this did not work I tried
> adding one to O1, but I kept getting the following error:
> "Atom H1 in residue 22 not found in rtp entry with 19 atoms..."
> Thank you in advance,
> Hotmail: Trusted email with Microsoft’s powerful SPAM protection.
> Sign up now. --
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users