> On Feb 8, 2015, at 1:01 PM, Ibrahim Said <saidibrahim569.gmail.com> wrote:
>
> Dears
> It is simply, I want to add a guanidine molecules to a unit contains my
> protein. What I have done, is th following
>> loadAmerparams Gdm.frcmod
> reading forcefield modification type file (frcmod)
> reading title:
> remark goes here
>> loadAmberprepi Gdm.prepi
> loading prep file ./gdm.prepi
>> source leaprc.gaff
> Loading parameters: /../../amber12/dat/leap/parm/gaff.dat
>> r = loadpdb Gdm-6M.pdb
> Loading PDB file: ./Gdm-6M.pdb
>> source leaprc.ff12SB
> Source: /../../amber12/dat/leap/cmd/leaprc.ff12SB
> ----- Source of /../../amber12/dat/leap/cmd/leaprc.ff12SB done
>> w = loadpdb myprotein.pdb
> total atoms in file: 3069
> Leap added 3328 missing atoms according to residue templates:
> 1 Heavy
> 3327 H / lone pairs
> then
>> add w r
> add: Argument #2 is type Unit must be of type: [molecule residue atom]
> usage: add <unit/residue/atom> <unit/residue/atom>
> There is something wrong I can not catch. please, can you help me.
The error message says what went wrong -- “r” must be a residue, not a UNIT. [1] I’ve never personally used the “add” command before (here is the help):
> help add
add a b
UNIT/RESIDUE/ATOM _a_
UNIT/RESIDUE/ATOM _b_
Add the object _b_ to the object _a_. This command is used to place
ATOMs within RESIDUEs, and RESIDUEs within UNITs.
Instead of “add”, try “combine”. A word of caution here, though: tleap is stupid when it comes to combining two units -- all it does is paste the two of them together. So the only way that ‘combine’ will work is if the starting coordinates for both units are compatible with each other (for instance, if both units came from the same PDB file, but split in two). Otherwise, tleap will put the guanidine molecule on top of whatever else happens to exist at those coordinates from unit ‘w’.
system = combine {w r}
Then, ‘system’ will be the unit with the combined coordinates of both w and r.
HTH,
Jason
[1] In case you were curious, the add command could *probably* be changed to “add w r.1” -- r.1 is the 1st residue of the ‘r’ unit (since ‘r’ has only one residue, it is also the entire unit). Although I would still advocate the use of “combine” instead, or, better yet, just use a PDB file that contains *both* the guanidine and the protein together and use that.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Feb 08 2015 - 13:30:02 PST
