From: Life Sciences Inc (contact.lifesciences.inc_at_gmail.com)
Date: Thu Oct 20 2016 - 08:55:53 CDT

Hi

Thanks for the help

I simulated my system using NAMD , in following ways

1) I simulated Lipid bilayer + water ( I used charmm GUI for this system to
have my starting structure and pdb file, and ran the simulations without
any trouble)

2) Simulated Lipid bilayer + water + some flourophore ( to create this
system I used vmd, first did solvation after measuring minmax values and
putting those values in the solvation tool, In this case I needed more
water along z axis so I added 12 Angstrom more along the z axis using the
box padding option solvation tool of vmd, after the solvation was complete
I had the system with Lipid Bilayer + water molecules new ones added on old
ones + flourophore and this system's pdb file was given to autopsf tool of
vmd and I added same top_all36_lipid.rtf file as a topology firl for
charmm36 ff and cgenff for small molecule, and autopsf made the psf and pdb
which I used in my simulation input files to run the equiliberation,
production in namd without any trouble

3) Now I am trying to make a pore in bilayer which is the first system
mentioned as 1 , I am doing the same thing as point 2 but without adding a
cgenff force field and using the same charmm36 lipid force field topology
file, I did the same measure min max but in this case I was aready
simulating the system so the x y and z coordinates changed and I added
those new coordinates in solvation tool of vmd and also in this case I need
more water so I did box padding of 20 Ang, Solvation tool gave me the
normal Psf and pdb file, but now I am having trouble in making the final
psf and pdb files from autopsf (where I have to add the forcefield for all
my system including lipids and water).

I also tried to just to take out the water molecules separately in a pdb
file and lipid bilayer in a separate pdb file and tried to add the same
charmm36 force field separately and then later on I had to append both psf
and pdbs from autopsf, but at the first step where I was adding force field
to only water molecules again the autopsf got held without displaying any
error.

Peter is also right that because it has to make many chains of water and
usually autopsf is done before doing solvation, but this thing is making me
confused big time that like this way how we are going to add force field
for water molecules? (as for simulating the system you need to add force
field for each and everything inside the system).

Thanks

On Thu, Oct 20, 2016 at 3:49 AM, Ashar Malik <asharjm_at_gmail.com> wrote:

> Not sure how you were simulating in the first place but normally Crystal
> structures have some water which are basically nascent oxygen atoms ... You
> convert them to some water representation (mostly tip3p) .. Are you sure if
> this was done correctly?
>
> To simulate any system irrespective of whatever it's contents are, you
> need to define it in terms of "A forcefield" ... If you use NAMD you will
> create a PDB and a PSF. Then using both of these files and the respective
> parameters you simulate.
>
> Having said that, to add more waters to a system already having waters
> (assuming you are using the GUI) you will have to fill in some boxes
> (either the length of the box after solvation or how much to solvate in
> each direction). I believe vmd solvates the entire box and then deletes all
> waters within a certain cutoff of your previous system. One approach is to
> delete the crystal structure waters and all the solvent using some
> solvation protocol. You can also retain the crystal waters assuming correct
> selections are made.
>
> For every change in the system even by one atom the pdb changes and as its
> coupled with the psf the psf must change as well. Doesn't matter what that
> change is. So you have to generate a new PSF for its corresponding pdb
> Everytime you delete/add something.
>
> Please tell us how you are adding new waters, what values are you putting
> into the GUI? A quick way to check is to add little solvent to see if some
> waters get added? Trouble shooting is a lot easier with the command line.
> Once you go through this and try out new things and if they don't work come
> back and I can give you a script to add some solvent running which you will
> have some output and we can better trouble shoot the problem then, if it
> occurs. In your next post do answer the questions I asked above.
>
> Best,
> /A
>
> On Oct 20, 2016 12:04 PM, "Life Sciences Inc" <
> contact.lifesciences.inc_at_gmail.com> wrote:
>
>> Basically I had a system who I was simulating already (lipids + water )
>> so I added force field and created psf and pdb, then later on I felt to add
>> more water in the already running system I stopped simulating it and then
>> added more water, by seeing different tutorials I noticed that yes
>> Solvation should be the next step after running autopsf (and also it takes
>> long time) but I was afraid that as I have added new water molecules so I
>> have to again add force field, thats why I added water molecules first and
>> then run autopsf to add forcefield and to get new psf and pdb files (but
>> the screen is getting held without any response, I tried with ions and
>> water.str file combined with force field then autopsf is running and making
>> the psf and pdb files, but also deleting many of the water molecules)
>>
>> for future reference:
>>
>> that means I don't have to add force field again whenever I am just
>> adding new water molecules in the system ? I have to add force field when I
>> add protein or some other molecule, is that right ?
>>
>> On Wed, Oct 19, 2016 at 11:33 PM, Life Sciences Inc <
>> contact.lifesciences.inc_at_gmail.com> wrote:
>>
>>> Basically I had a system who I was simulating already (lipids + water )
>>> so I added force field and created psf and pdb, then later on I felt to add
>>> more water in the already running system I stopped simulating it and then
>>> added more water, by seeing different tutorials I noticed that yes
>>> Solvation should be the next step after running autopsf (and also it takes
>>> long time) but I was afraid that as I have added new water molecules so I
>>> have to again add force field, thats why I added water molecules first and
>>> then run autopsf to add forcefield and to get new psf and pdb files (but
>>> the screen is getting held without any response, I tried with ions and
>>> water.str file combined with force field then autopsf is running and making
>>> the psf and pdb files, but also deleting many of the water molecules)
>>>
>>> for future reference:
>>>
>>> that means I don't have to add force field again whenever I am just
>>> adding new water molecules in the system ? I have to add force field when I
>>> add protein or some other molecule, is that right ?
>>>
>>> On Wed, Oct 19, 2016 at 9:25 PM, Peter Freddolino <petefred_at_umich.edu>
>>> wrote:
>>>
>>>> When you say that it is getting held, is there any output going to the
>>>> console? Do you have an hourglass/spinning lollipop/busy indicator for your
>>>> mouse cursor when vmd is active? How long have you waited?
>>>> The ideal workflow is to run autopsf and THEN run solvate. Autopsf will
>>>> take a LONG time on a solvated system because it has to run chain splitting
>>>> on all of the waters…
>>>>
>>>> Best,
>>>> Peter
>>>>
>>>> > On Oct 19, 2016, at 12:13 PM, Life Sciences Inc <
>>>> contact.lifesciences.inc_at_gmail.com> wrote:
>>>> >
>>>> > HI ALL
>>>> >
>>>> > I am trying to create a psf file and pdb file from autopsf , I am
>>>> addding the charmm 36 force field for lipid and water molecules through
>>>> topology file "top_all36_lipid.rtf". First I did solvation using Solvate
>>>> tool of vmd and then I am loading the pdb file from solvate tool to be used
>>>> in autopsf tool.
>>>> >
>>>> > Autopsf is making chains and everything is normal, but when the
>>>> processing comes to the last chains of TIP3 water molecules somehow the
>>>> tool is getting held and showing no error. I am using VMD 1.9.2 version.
>>>> >
>>>> > Is there any solution for this?
>>>> >
>>>> > Thanks
>>>> >
>>>> >
>>>> >
>>>>
>>>>
>>>
>>