VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Fri Mar 27 2020 - 17:17:58 CDT

This is a VMD question, so I’m dropping namd-l from the reply.

You have at least one segment with a five-character name (LO111). This gets truncated in the pdb file, so psfgen can’t associate the atoms correctly between the two. In general, you should keep your segnames to four characters. However, a way around that is to force psfgen to assume there is a 1-1 correspondence between the files by using

readpsf ___.psf pdb ____.pdb <— I confirmed this worked.

Best,
JC

> On Mar 27, 2020, at 12:42 AM, jiali wang <jialiwangnamd_at_gmail.com> wrote:
>
> Dear VMD users,
> I generated a POPC lipids exvironment with water and Sodium. however when I trying to merge the structure, I found the lipids could not read by VMD?
> what I did is using following command to merge structure.
> "readpsf lipids_autopsf.psf"
> "coordpdb lipids_autopsf.pdb"
> it's not working and says:
> psfgen) Warning: failed to set coordinate for atom C316 POPC:30 LO10
> psfgen) no segment LO10
> Do you know what happened?
> Thank you!!
> Jiali
>  lipids_autopsf.pdb <https://drive.google.com/file/d/1JEc52zeJzMIRY8mWoNnPBbFhtgJepSLK/view?usp=drive_web>
>  lipids_autopsf.psf <https://drive.google.com/file/d/1RrcmV89L3vT94gNivBD8nIf6--W6AzK2/view?usp=drive_web>