AMBER Archive (2002)

Subject: check-up question

From: Cozmuta (ioana_at_wag.caltech.edu)
Date: Tue Aug 06 2002 - 14:13:31 CDT

Hi Amber users,

I just want to make sure I understand the message given by Amber.

The protein I am trying to work on has 7 independent chains that start
with ALA and end with ASN. I removed all protons on the X-ray .pdb
structure and let xleap to add the hydrogens back. When I want to save the
new pdb structure with saveAmberParm I get the following message:
Residues lacking connect0/connect1 don't have chain types marked:
        residues total affected
        CASN 7
        NALA 7

According to the unit.c executable this is only a warning (and to me it
seems reasonable that the program does not know how to connect these ends
that actually should not be connected). According to the same executable:
"Join the two UNITs together into a sequence, meaning
 * if they both have connect atoms defined for LASTEND and FIRSTEND
 * then connect them. If only one has its connect atom defined
 * then print a warning and join them,
 * and if neither has its connect atom defined
 * then simply join the UNITs."

So this means that there is no error in the structure and the 7 units are
treated (and saved as well in the topology and coordinate file) as
independent.

Is my understanding correct?

Additionally I also have a question. Leap is also warning me that
The unperturbed charge of the unit 7 is not zero
meaning that my structure bears a charge of +7. However if I load the same
file in another program (InsightII) and use the amber ff, the total charge
on the structure is zero. I tried to look into the code
($AMBERHOME/src/leap/src/leap/unit.c) but I could not figure out how this
charge was obtained and which residues have the charge that does not
compensate. I would appreciate any useful hints that would help me
understand this.

Thank you in advance,
Ioana