[gmx-users] Re: pdb2gmx fatal error - atom not found
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 23 16:37:10 CEST 2011
C Colenso wrote:
> Hi Justin,
> I got your email from the Gromacs mailing list...I hope you don't mind.
> I have a problem with pdb2gmx.
> I have downloaded the 4.5.4 version of gromacs, no luck, I have consulted
> the mailing lists and bugzillas, and tried every suggestion but this is
> still not fixing my problem and I am getting rather frustrated now....
> Please could you try and help....?
I cannot serve as a private tutor; I reply to the list for the benefit of the
community and to further discussion. I receive far too many personal requests
to keep up with them all. I am CC'ing this message to the gmx-users list and
would ask that you post anything further there. That's why the mailing list exists.
> I am trying to output a .pdb from a .gro file using this command:
> pdb2gmx -f herg_popc_L532P_md-2.gro -o herg_popc_L532P_md-2.pdb -chainsep
> id -ter
This command will not work. There are no chain identifiers in a .gro file, so
this could be one source of breakdown.
> (I have tried using the -interactive and -ignh commands but this doesnt
> help either)
Without seeing the remaining selections (force field, termini selection) I can't
comment further about whether you're doing things right.
> The error message I get is:
> Fatal error:
> Atom OXT in residue ALA 671 was not found in rtp entry ALA with 10 atoms
> while sorting atoms.
This may be a consequence of the -chainsep option identifying something
incorrectly. Is there anything else in the input coordinate file after Ala671?
It appears from the coordinates below that it should indeed be a terminus, but
there could be some confusion if there are other things in the .gro file.
> I have tried adding OXT to the .rtp...this didnt work
Nor should it. Termini replacements are made by the .n.tdb and .c.tdb files;
they handle renaming and atom addition/deletion. You shouldn't need to change
> This is a problem with the C-terminal ALA residue.....
> This is what it looks like in the .gro:
> 671ALA N 4423 9.361 10.928 5.227 0.1453 -0.0243 -0.1436
> 671ALA H 4424 9.377 11.023 5.197 1.0816 0.3382 1.3859
> 671ALA CA 4425 9.270 10.924 5.340 0.0567 -0.1974 -0.2220
> 671ALA HA 4426 9.199 10.841 5.341 -2.2883 1.6603 -1.8477
> 671ALA CB 4427 9.339 10.922 5.476 0.1011 -0.2943 -0.2457
> 671ALA HB1 4428 9.267 10.946 5.555 1.2607 0.1822 0.7063
> 671ALA HB2 4429 9.373 10.818 5.475 1.9064 0.2650 -1.6416
> 671ALA HB3 4430 9.430 10.981 5.484 -0.8386 1.2073 -0.3433
> 671ALA C 4431 9.178 11.045 5.338 -0.3791 -0.5290 -0.3389
> 671ALA OT 4432 9.212 11.144 5.274 -0.3511 -0.0384 0.4190
> 671ALA O 4433 9.074 11.040 5.426 0.0589 -0.2978 0.1970
> 671ALA HO 4434 9.082 10.962 5.479 -1.1979 0.0008 0.8966
> I don't know what is going on with the C-term and why there are so many
> atoms.....OT,O and HO
That's a normal (protonated) C-terminus. OT is the carbonyl O, and O and H are
the acidic portion of the -COOH terminus.
> If you could offer any suggestions I would be most grateful, I hope I have
> given you enough info...
> Many thanks in advance
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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