From: Olena Dobrovolska <>
Date: Wed, 28 Mar 2012 15:40:02 +0000

Thank you, David, I agree about COM problems. I think it comes from pseudoatoms in upl file and if I set it more specific (HB2, HG2, etc.) I reduce COM atoms.
But as you can see there in Final results part there are CB, CG atoms, whereas, there should be protons, as it is in dist file. I checked my RST file and found that there is a problem: sometimes the atom number doesn't correspond to the atom name, for example,
# 30 LEU QQD 85 VAL QQG 4.38 (#peak 1066)
  ixpk= 1066, nxpk= 0, iat= 74, 967, r1= 1.30, r2= 1.80, r3= 4.38, r4= 4.88, &end
but in my pdb file 967 number has CB atom of VAl 85. And this mess is not regular, so I can't figure why it creates RST file in such way.
I attached the RST, pdb and dist files. Please, check what is wrong there.


From: David A. Case []
Sent: 28 March 2012 16:53
To: AMBER Mailing List
Subject: Re: [AMBER] COM

On Tue, Mar 27, 2012, Olena Dobrovolska wrote:
> in the final results part there is this COM instead of the a certain
> atom name as it should be.

Can you be more specific? I don't see any "COM" in the final results section
of your output. COM stands for center of mass, and you have lots of groups of
atoms (mostly methyls) where the constraint is to the center of mass of
several atoms.

> I also have a huge (663) distance penalty
> value, although the CYANA output files, used in AMBER as inputs, have
> target function around 4, and RMSD 0.5.

You total distance penalty is made up of many values that are 20 or 30 or
so, with only the sum coming up to 663. You probably need to examine the
biggest restraint violations(which involve distances of about 1 Ang) to
see if there might be typos in the RST file, or similar problems.

Good luck....dac

AMBER mailing list

AMBER mailing list

Received on Wed Mar 28 2012 - 09:00:04 PDT
Custom Search