[gmx-users] UNK not found in residue topology

[Janowicz, Adrianna C.]

Hello,

I'm getting an UNK not found in residue topology error message.
I figured out what the error was and tried to add carbon to ffopslaa.rtf
but it was unsucessful.

What can I do/How can I change my pdb file from UNK so that Carbon and
Hydrogen can be recognized? (I built my own hydrocarbon strucutre and
added it to an existing PDB file).

Thanks,
Adrianna

[Justin A. Lemkul]

Post by Janowicz, Adrianna C.
Hello,
I'm getting an UNK not found in residue topology error message.
I figured out what the error was and tried to add carbon to ffopslaa.rtf
but it was unsucessful.
What can I do/How can I change my pdb file from UNK so that Carbon and
Hydrogen can be recognized? (I built my own hydrocarbon strucutre and
added it to an existing PDB file).

I think you need to be a bit more specific about what you're trying to do. Are
you getting errors from pdb2gmx or some other tool? If so, what are they?
Otherwise, the only requirement for proper processing is that the PDB format be
retained and that the atom names match what is expected in the .rtp file.

-Justin
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

[Janowicz, Adrianna C.]

Hello,

I'm getting an UNK not found in residue topology error message.
After I run
pdb2gmx -f XXX.pdb -o conf.pdb

Fatal error:
Residue 'UNK' not found in residue topology database


I figured out what the error was and tried to add UNK as carbon to
ffopslaa.rtf

[UNK]
[ atoms ]
UNK UNK 0.000 0

but I am still getting the same error. What do I do?

Adrianna

[Justin A. Lemkul]

Post by Janowicz, Adrianna C.
Hello,
I'm getting an UNK not found in residue topology error message.
After I run
pdb2gmx -f XXX.pdb -o conf.pdb
Residue 'UNK' not found in residue topology database
I figured out what the error was and tried to add UNK as carbon to
ffopslaa.rtf

There are no .rtf files used by Gromacs, so if you've created or edited one, it
will have no effect.

Post by Janowicz, Adrianna C.
[UNK]
[ atoms ]
UNK UNK 0.000 0
but I am still getting the same error. What do I do?

In theory, one can define a residue named UNK with atom names and types of UNK,
but that's an incredibly awkward mechanism. It would probably be worthwhile to
use real, existing atom types (which would be required by OPLS) with a
meaningful residue name. Perhaps the format of your .pdb file is wrong and
pdb2gmx is reading another column for the residue name instead of the one
intended. If you specify everything as UNK, you'll never know.

-Justin
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================