RE: angle deformation

From: JC Gumbart (
Date: Thu Dec 18 2008 - 23:04:17 CST

They fluctuate wildly because they are not specified in your PSF. In your
psfgen script, add the following line after using the patch statement:


regenerate angles dihedrals


PSFgen autogenerates the angles and dihedrals ONLY when building the
segment, or when it is explicitly told to do so like above.



From: [] On Behalf
Sent: Wednesday, December 17, 2008 5:01 PM
To: NAMD list
Subject: namd-l: angle deformation


Hi everybody
I am simulating a small ligand using topology/parameter files modified by
analogy with other parameters available in the original files. The initial
topology of the molecule is OK but as soon as MD starts the angle C-OT2-CT
gets deformed to wild values (jumping between 150 and 120 degrees instead of
the theoretical 109) and also the angles HT-CT-HT (jumping between 10 and
150 degrees during a simulation instead of the theoretical 110 degs). The
choices I made when modeling the missing parameters looked intuitively
correct to me, so now I am a bit stucked. I know that tampering with the
topology/parameter files is done 'at my own risk' but any ideea about why I
am getting this wild behaviour would be very appreciated.
Please find attached the links to the modified topology (with new atom names
HJx for the NTER patch), parameter file (the new entries are commented with
'analogy...' on the second comment line) and the psf and pdb files of the


Excerpts of the new entries from the parameter file:


HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd
                ! analogy based on HA CT2 HA

HC NH1 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
                ! analogy from HC NH3 CT1

HC NH1 HC 39.000 106.5000 ! ALLOW POL
                ! analogy from HC NH2 HC

NH3 CT1 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI
                ! analogy from NH3 CT1 C

HC NH1 CT1 CD 0.1100 3 0.00
                !analogy from HC NH2 CT2 CD

HC NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP
                ! analogy from H NH1 CT1 CT2
HC NH1 CT1 HB 0.1100 3 0.00
                !analogy from HC NH2 CT2 HB

Many thanks and warm regards


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