Re: angle deformation

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Dec 19 2008 - 19:11:38 CST

Hi Vlad,
 two things...

CHINDEA Vlad wrote:
> Dear James
>
> This was a revelation to me ! I could never imagine that angles and
> dihedrals might be missing from the PSF in the absence of any
> complaints from the MD program.
>
> Since my PSF was built with AutoPSF I have no script that I can adjust
> but I have tryed to do as suggested by you enter the following lines
> at the VMD prompt:
 From the autopsf documentation:
The "Regen" option will cause psfgen to regenerate all angles and
dihedrals from connectivities prior to writing the psf. Note that this
step is generally not necessary, but is needed with early generations of
CMAP-based topology files if your molecule includes any patches.

You could try again using the regen option.
>
> topology <file>
> regenerate angles dihedrals (here I got the message:
> regenerating all angles, dihedrals)
> set sel [...all]
> $sel writepsf....
>
> but PSF file was generated with no angle, dihedral or improper
> information ! Any ideeas on what might be wrong ?
The way to write a psf from psfgen is:
writepsf filename
$sel writepsf uses the molfile plugin for psf files, which does not
write angles, dihedrals, or impropers.

Peter
>
> If all fails I imagine that I could add the missing angles and
> dihedrals by hand in the PSF file. Are there any issues with this
> approach ? Of course I would have to take care of the total no. of
> angles (dihedrals) and proper no. of items/line.
>
> Many thanks and kind regards
>
> Vlad
>
>
> From: gumbart_at_ks.uiuc.edu
> To: vchindea_at_hotmail.com; namd-l_at_ks.uiuc.edu
> Subject: RE: namd-l: angle deformation
> Date: Thu, 18 Dec 2008 23:04:17 -0600
>
>
> 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:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *CHINDEA Vlad
> *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 ligand.
>
> http://rapidshare.com/files/174371793/STME.pdb
>
>
> http://rapidshare.com/files/174371794/STME.psf
>
>
>
> http://rapidshare.com/files/174371795/par_all27_prot_lipid_na_mod.inp
>
>
>
> http://rapidshare.com/files/174371796/top_all27_prot_lipid_na_mod.inp
>
>
>
> 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
>
> Vlad
>
>
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