From: Vermaas, Joshua (
Date: Wed Oct 09 2019 - 08:51:59 CDT

Check the wrapWater documentation. This is perfectly normal, depending on what the origin is.


On 2019-10-09 03:42:58-06:00 Amir Suhail wrote:

Thank you sir, that works. I have one more question. I am starting my simulation with periodic water box of known dimensions at one end as shown at top in attached figure. I am applying pbc according to water box dimensions in NAMD. Even just after one MD step after equilibration the system changes to one shown at bottom in attached figure. Why water box suddenly comes in middle ?
Is this visualization problem or something ?
Thank you,
- Amir Suhail

Research Fellow,
Theoretical Physics,
The Institute of Mathematical Sciences,
Chennai, India.

On Mon, Oct 7, 2019 at 7:32 PM Vermaas, Joshua <<>> wrote:
Yeah, its the -1408 that is causing problems. PDB files only allow for 4 digits before the decimal point. The minus sign makes it 5. Translate the system and you'll be fine. $sel moveby [vecscale -1 [lindex [measure minmax $sel] 1]] or something similar to that will work.


On 2019-10-04 23:58:21-06:00 Amir Suhail wrote:

Hi Joshua,
My system is extended along z-axis consist of total 96330 atoms with solvent. After translating system's center of mass to origin, following are my minmax coordinates :-
min :- {-25.08873748779297 -37.81959533691406 -1408.67724609375}
max :- {44.35075378417969 21.350582122802734 1282.7738037109375}

On Thu, Oct 3, 2019 at 10:14 PM Vermaas, Joshua <<>> wrote:
Hi Amir,

How big is your system? This error crops up when any of the fixed format fields can't be written, usually when an atomic coordinate gets to be more than 10000 or less than -1000. Would this be true in your case after translation? If so, using pbctools to rewrap the coordinates would be the next step forward.


On 2019-10-03 05:44:31-06:00<> wrote:

Hi all,

I selected my molecule and used writepdb to convert .coor to pdb file but vmd is giving following error :-

PDB WRITE ERROR: Position, occupancy, or b-factor (beta) for atom 0
                                 cannot be written in PDB format.
                                 File will be truncated.

This has been discussed in mailing list :-
I shifted the origin to center of mass and set occupancy and beta to zero according to answer in above link but still I am getting writepdb failed error.

Thanks in advance,