VMD-L Mailing List

From: Ivan Gregoretti (ivangreg_at_gmail.com)
Date: Sun Oct 13 2024 - 14:29:22 CDT

Hello Mustafa.

I am unable to solve the problem with the Automatic PSF Builder, however,
if you are open to alternative solutions, I can offer two.

1) PDBFixer

/path/to/pdbfixer \
/path/to/1dqj_fromCIF.pdb \
--add-atoms=all --ph=7.0 \
--output /path/to/1dqj_H.pdb

2) pdb2pqr

# Addition of missing hydrogens is accomplished as a file subproduct of the
# creation of a `.pqr` file.
/path/to/pdb2pqr \
--ff CHARMM --titration-state-method propka --with-ph 7.0 --quiet \
--pdb-output /path/to/1dqj_H.pdb \
/path/to/1dqj_H.pqr

rm /path/to/1dqj_H.pqr

I hope this helps. If it does, please let the users in this list know.

Ivan

On Sun, Oct 13, 2024 at 1:36 PM Mustafa Tekpinar <tekpinar_at_buffalo.edu>
wrote:

> Hello everybody,
>
> We are trying to use VMD 1.9.3 on Windows 10 (and 11) for adding missing
> hydrogen atoms with Automatic PSF Builder. Unfortunately, we get the
> following error:
> Unable to open file {.\p53_isoform5_model0_autopsf_preformat_protein.pdb
> for writing
> Obviously, it is a file writing problem. I was wondering if anyone can
> suggest a solution to this problem.
>
> Thanks in advance,
> Mustafa
>
> Mustafa Tekpinar, PhD
> Associate Professor of Physics
>
> Van Yuzuncu Yil University
> Department of Physics
> Faculty of Science
> Kampus, Van, 65080
> TURKEY
>
>
>