if you look at your PDB file, you'll see that there are H atoms listed only
for NLEU, not for any other residue. also, these H atoms all have the same
name. Perhaps you might want to look into the source of this pdb file, and
see if those H atoms really should be in your file or not. If so, you need
to tell Amber which atom each of these H's are, since it doesnt' really
have a way to figure it out if the names are all just "H".
On Fri, Sep 26, 2014 at 11:21 AM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Dear Amberists;
>
> I am running tleap using AMBER 12 with the following script on a receptor
> which is attached herewith. During running the Leap I am encountering this
> problem
>
> "
> FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> Writing pdb file: rec_solvated.pdb
> Converting N-terminal residue name to PDB format: NLEU -> LEU
> Converting C-terminal residue name to PDB format: CLEU -> LEU
> Quit
> "
>
> I would highly appreciate any response in this regard.
> Thank you for all your time.
>
>
> tleap.in
>
> source leaprc.ff99SB
> receptor = loadPDB rec.pdb
> saveAmberParm receptor rec.top rec.crd
> charge receptor
> addIons2 receptor Cl- 0
> solvateBox receptor TIP3PBOX 8.0
> saveAmberParm receptor rec_solvated.top rec_solvated.crd
> savepdb receptor rec_solvated.pdb
> quit
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
> Researcher
> Molecular Modelling and Drug Design Research Group
> Discipline of Pharmaceutical Sciences
> UKZN, Westville
> Weblink: http://soliman.ukzn.ac.za/Home.aspx
> Past: Department of Pharmaceutical Sciences
> Birla Institute of Technology, Mesra, India
> in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Sep 26 2014 - 08:30:03 PDT
