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

From: Kostas Bourandas <k0stasmp123.gmail.com>
Date: Sat, 6 Aug 2016 13:32:44 -0700

Hello all,

I have some questions regarding how to connect 2 molecules: one polypeptide
and a PEG chain.

I downloaded the polypeptide's structure directly from rcsb database(NMR).

When I loadpdb the file I got about 160 warnings for atom proximities.

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

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.

Is it correct?

Secondly, I connect the NH2 of my PEG chain to the NH2 of the
polypeptide(delete one NH2, kept the other and made the connections, fixing
the charge as before-there is no program Sirius to follow the instruction
of the tutorials)

Is it proper to modulate my molecules' charge like that?Is there a limit
that I could add or substract from an atom to make the whole charge an

After I have my polypeptide-PEG complex I saveamberparm to save prmtop and
inpcrd files and although it was succesful I got a warning about the length
of the bond between PEG and polypeptide which I draw manually.

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?
If I use the prmtop file for MDs will I have a problem?

Could you please tell me if I am using the right techniques here?


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Received on Sat Aug 06 2016 - 14:00:03 PDT
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