Re: psfgen error protein-ligand

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Fri Oct 04 2019 - 10:41:31 CDT

I suspect that the str file has a different resname mostly "/tmp/php"
,search for this and change everywhere with "UNK" .

Thank you.

On Fri, Oct 4, 2019 at 1:13 PM Pavel Kostadinov <pkcre_at_abv.bg> wrote:

> Dear NAMD users,
>
> I have been trying to run psfgen for a protein in question (albumin) and a
> ligand (diisocyanate) from a docking pose. I have parameterized my ligand
> with CGenFF and downloaded the CHARMM topology and parameter files required
> for the psfgen run. However, on running the plug-in I obtained a warning
> that psfgen failed to set coordinates for the atoms:
>
> psfgen) Warning: failed to set coordinate for atom O UNK:0 XO1
> psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1
> psfgen) Warning: failed to set coordinate for atom N UNK:0 XO1
> psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1
> psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1
> psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1
> psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1
> psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1
> psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1
> psfgen) Warning: failed to set coordinate for atom N UNK:0 XO1
> psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1
> psfgen) Warning: failed to set coordinate for atom O UNK:0 XO1
>
> Then I decided to change the names of the heteroatoms in the .pdb file
> (from C,O,N to C1,O2,N1 - the way I find them in the .str file) since they
> might not be CHARMM appropriate. On doing that, however, the correct
> docking pose is lost, BUT!!! I managed to create .psf file for this wrong
> pose. Still, I receive warning that coordinates for hydrogen atoms, which
> are not included in the pdb, are poorly guessed.
>
> psfgen) Warning: poorly guessed coordinate for atom H1 UNK:0 XO1
> psfgen) Warning: poorly guessed coordinate for atom H2 UNK:0 XO1
> psfgen) Warning: poorly guessed coordinate for atom H3 UNK:0 XO1
> psfgen) Warning: poorly guessed coordinate for atom H4 UNK:0 XO1
> psfgen) Warning: poorly guessed coordinate for atom H5 UNK:0 XO1
> psfgen) Warning: poorly guessed coordinate for atom H6 UNK:0 XO1
> psfgen) Warning: poorly guessed coordinate for atom H7 UNK:0 XO1
> psfgen) Warning: poorly guessed coordinate for atom H8 UNK:0 XO1
> psfgen) Warning: poorly guessed coordinate for atom H9 UNK:0 XO1
> psfgen) Warning: poorly guessed coordinate for atom H10 UNK:0 XO1
> psfgen) Warning: poorly guessed coordinate for atom H11 UNK:0 XO1
> psfgen) Warning: poorly guessed coordinate for atom H12 UNK:0 XO1
>
> I have tried many things: from writing separate .str files from the one I
> obtained from CGenFF to changing the residue names in the pdb file, but
> nothing seems to work. How to change the pdb file in such a way so I don't
> lose my docking pose and the CHARMM files (and NAMD) recognize the ligand?
>
> Thank you in advance, I appreciate your willingness to help!
>
> Greetings,
> Pavel.
>

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*

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