[gmx-users] Error by pdb2gmx
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 29 00:37:04 CEST 2009
Yanmei Song wrote:
> Dear All users:
>
> I was trying to set up a long chain polymer system. I got the
> following PDB file from WebLab. How can I make changes to the file in
> order to make it as a GROMACS input pdb file. Then I can use pdb2gmx
> to get the gro, itp and top file.
>
> When I perform the pdb2gmx command, I got the error message:
>
> Residue 'MOL' not found in residue topology database
>
You can't expect pdb2gmx to be magic. A simple search of the list archives and
wiki will turn up the following:
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
-Justin
> Thank you in advance!
>
> REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009
> ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00
> ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00
> ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00
> ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00
> ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00
> ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00
> ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00
> ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00
> ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00
> ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00
> ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00
> ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00
> ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00
> ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00
> ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00
> ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00
> ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00
> ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00
> ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00
> ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00
> ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00
> ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00
> ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00
> ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00
> ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00
> ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00
> ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00
> ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00
> ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00
> ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00
> ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00
> ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00
> ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00
> ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00
> ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00
> ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00
> ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00
> ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00
> ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00
> ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00
> ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00
> ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00
> ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00
> ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00
> ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00
> TER
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list