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

From: Kostas Bourandas <>
Date: Mon, 8 Aug 2016 19:56:53 -0700

Thank you very much for your replies David!!

I am just downloading a single pdb file from rcsb (e.g a protein-ligand
complex, no multiple conformations) and in xleap I do

"prt_lig=loadpdb protein-ligand.pdb"

When I do "check prt_lig" I get many warnings concerning proximities.

But even when I do something like "prt-lig=sequence{ACE ASP ARG GLY GLY GLY
... NHE}"

and I do "check prt-lig" I might still get the same kind of warnings. I
then usually do "edit prt-lig" and I manually put some distance between
side chains and the warnings reduce.

It is true though that I haven't used pdb4amber tool to choose model

As far as concerns the CLeu, when I use loadpdb amber creates Cleu from Leu
automatically. I just wanted to add NHE cap so as to connect it with PEG's

I used the command prt-lig_new=sequence{prt-lig NHE}, then manually erased
the oxygen from CLeu, and modified the charges so as to have an
integer total charge after the oxygen deletion and NHE addition.

Then I manually erase NH2 from PEG, modified its charges, and I connect
what remains to prt-lig so as to have a new prt-lig-peg molecule with
integer charge.

Is this the correct way to work?


2016-08-06 19:27 GMT-07:00 David A Case <>:

> 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.
> ....dac
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Received on Mon Aug 08 2016 - 20:00:02 PDT
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