On Tue, Dec 9, 2014 at 4:59 PM, Wong, Sook (NIH/NCATS) [V] <
sook.wong.nih.gov> wrote:
> Hi,
>
> I am trying to generate prmtop & inpcrd using tleap. However, I am
> encountering the following issues:
> FATAL: Atom .R<LIG 393>.A<C1 1> does not have a type.
> FATAL: Atom .R<LIG 393>.A<C2 2> does not have a type.
> FATAL: Atom .R<LIG 393>.A<C3 3> does not have a type.
> FATAL: Atom .R<LIG 393>.A<C4 4> does not have a type.
> FATAL: Atom .R<LIG 393>.A<C5 5> does not have a type.
> FATAL: Atom .R<LIG 393>.A<C6 6> does not have a type.
> FATAL: Atom .R<LIG 393>.A<C7 7> does not have a type.
> FATAL: Atom .R<LIG 393>.A<C8 8> does not have a type.
> FATAL: Atom .R<LIG 393>.A<C9 9> does not have a type.
> FATAL: Atom .R<LIG 393>.A<C10 10> does not have a type.
> FATAL: Atom .R<LIG 393>.A<C11 11> does not have a type.
> FATAL: Atom .R<LIG 393>.A<C12 12> does not have a type. Etc.
>
> I have enclosed the log from tleap as well as my com.pdb. Can anyone
> advise the issue?
>
You need to build a residue library for your ligand residue. Antechamber
is usually used for this step. Note that you MUST have all hydrogen atoms
added to your model before using antechamber (it looks like your LIG
residue only has carbon atoms).
Have a look through the Amber tutorials at
http://ambermd.org/tutorials/ --
several involve parametrizing a new residue using antechamber and should be
of help to you.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Dec 09 2014 - 18:30:03 PST
