From: JC Gumbart (
Date: Mon Mar 30 2020 - 12:48:52 CDT

Hi Jiali,

If you’re referring to the files you attached, there are still some segments with five-character names. I guess you looked at the PDB, where it gets truncated.

The difference between the two psfgen commands is like I said, in how it chooses to match up atoms, whether by segname or 1-1.


> On Mar 27, 2020, at 11:27 PM, jiali wang <> wrote:
> Dear JC,
> Thank you so much for your reply.
> I found another lipids file. I carefully checked all segnames are four characters. However, there are two segname L010(after L099, next should be L0100, but psfgen named L010), VMD couldn't read the file by "coordpdb lipids.pdb". Do you know what happened in this case? So if psfgen truncated the fifth character, when I force the VMD to read it by "readpsf ___.psf pdb ____.pdb". will it merge two segname L010 together(the No.10 and No.100 segname)?
> Another question. I found by using "readpsf ___.psf pdb ____.pdb" it's working fine. Do you know what's the difference between "readpsf ___.psf pdb ____.pdb" and "readpsf ___.psf coordpdb ____.pdb"?
> Thank you so much for your help and your time!
> Jiali
> On Fri, Mar 27, 2020 at 3:18 PM JC Gumbart < <>> wrote:
> 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 < <>> 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 <>
>>  lipids_autopsf.psf <>
> <lipids.pdb><lipids.psf>