VMD-L Mailing List

From: jiali wang (jialiwangnamd_at_gmail.com)
Date: Mon Mar 30 2020 - 14:40:04 CDT

Hi JC,
Thank you for the clarification. I understand.
best,
Jiali

On Mon, Mar 30, 2020 at 10:48 AM JC Gumbart <gumbart_at_physics.gatech.edu>
wrote:

> 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.
>
> Best,
> JC
>
> On Mar 27, 2020, at 11:27 PM, jiali wang <jialiwangnamd_at_gmail.com> 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 <gumbart_at_physics.gatech.edu>
> 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 <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>
>>
>>
>> <lipids.pdb><lipids.psf>
>
>
>