Dear Amber users,
I made some progress but didn't achieve my goal completely.
I created a tip4pew.pdb file with the following contents:
ATOM 1 O TP4 1 12.718 8.873 8.539 0.000
ATOM 2 H1 TP4 1 12.637 7.958 8.269 0.524220
ATOM 3 H2 TP4 1 12.304 9.370 7.833 0.524220
ATOM 4 EPW TP4 1 12.654 8.820 8.414 -1.048440
TER
and used it with AddToBox to fill up with TIP4P-Ew waters a predefined box.
However, when I loaded it in VMD and checked the partial charges I found
the following inconsistencies:
0.0 0.5199998617172241 0.5199998617172241 -1.0399997234344482
instead of 0.0 0.5242198705673218 0.5242198705673218 -1.0484397411346436,
which is the value I get with TIP4P-Ew waters made with leap.
Perhaps the connectivity may be incorrect too, but I am not familiar with
the .prmtop format.
How can I load in leap TIP4P-Ew waters in a .pdb file and write a correct
.prmtop file?
I hope someone will help me this time.
Thomas
On 15 December 2012 01:02, Thomas Evangelidis <tevang3.gmail.com> wrote:
> Dear Amber users,
>
> I want to define a parallelepiped box with specific dimensions. After
> reading the numerous posts in the mailing list and the manual, I couldn't
> figure out the way to create a solvated box with the desired dimensions.
> The closer I could get was when I used the following commands in tleap:
>
> mol = loadpdb protein.pdb
> addIons2 mol Na+ 90 Cl- 110
> solvateBox mol TIP4PEWBOX { 40 40 40 }
> setBox mol vdw
> set mol box { 56 108 104 }
> savePDB mol protein.amber.pdb
> saveAmberParm mol protein.prmtop protein.inpcrd
>
> Although the last line of protein.inpcrd contains the right box
> dimensions, the total number of atoms is ~300K whereas the box I want
> contains just 82K atoms. How can I achieve that?
>
> thanks,
> Thomas
>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 17 2012 - 03:00:03 PST
