Re: [AMBER] Extend of manual modulation-Connectin​g two molecules methodology

From: David A Case <>
Date: Sat, 6 Aug 2016 22:27:23 -0400

On Sat, Aug 06, 2016, Kostas Bourandas wrote:
> I downloaded the polypeptide's structure directly from rcsb database(NMR).
> When I loadpdb the file I got about 160 warnings for atom proximities.

Does the RCSB file have multiple models in it? That might explain the
warnings (or might is impossible to tell without more information).
You should always run input pdb files through pdb4amber, whcih can help you
choose models.

> I used the sequence command to add ACE and NHE caps.

??? This sounds odd, but I don't know what coordinates you are extracting
from the PDB.

> I then loadpdb the file, erased the extra oxygen that was added to the last
> residue(CLEU) and I substracted the resulted difference in the total charge
> to the C atom to which it was connected.

I think you need to give more detailed information. If you added an NHE cap
to the end of the peptide, there should not have been any CLEU residue.
Remember the usual advice: tell us what you actually did, (i.e. the commands
you actually ran), not what you hoped to accomplish.

> Finally, when I used the ambpdb tool to have the resulted pdb file I got
> the structure but with many extra bonds.
> I guess they happen because of the proximities between atoms?Is there any
> way for these extra bonds to be avoided?

Please see above. See if you can understand in detail the warnings about
atom proximities. If the polypeptide part is problematic, it won't matter
what you did with the PEG.


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Received on Sat Aug 06 2016 - 19:30:02 PDT
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