* Wiadomość oryginalna *
Od:
mailmd2011.gmail.com
Wysłana:
09:05:15
14-11-2012
Do:
[AMBER Mailing List] amber.ambermd.org
Temat:
Re: [AMBER] problem for lipid GAFF
hello Ross and Igor:
thanks for kind advices. In fact my system was built from CHARMM-GUI
and it already contains all necessary water for a system, so I don't
need additonal water by tleap.
I even know how large is the pbc box. I am just wondering, is it
possible simply add the pbc box information to the system and my system
can be centered in the pbc box?
thank you very much
best
Albert
On 11/13/2012 07:23 PM, Ross Walker wrote:
> Hi Albert,
>
> You can just use the solvate box command for this. For example if you just
> want to use TIP3P water then in leap before saving the prmtop just issue
> the command:
>
> solvatebox mol TIP3PBOX 10.0
>
> This will add an orthorhombic box of water of 'thickness' 10 angstroms
> around your entire lipid. It will automatically be centered inside the box
> of water.
>
> All the best
> Ross
>
>
>
> On 11/13/12 9:12 AM, "Albert" <mailmd2011.gmail.com> wrote:
>
>> Hi Ross and Dickson:
>>
>> thanks a lot for such kind comments.
>> I used the "CHARMM-compatable" prameters, and it works fine now.
>> However, I've got a question, how can we add pbc box to the system? and
>> how can we center our system in the pbc box?
>>
>> thank you very much
>> best
>> Albert
>>
>>
>> On 11/13/2012 06:03 PM, Ross Walker wrote:
>>> Hi Albert,
>>>
>>> You don't state how your prepared g2a.pdb. It looks like your atom
>>> naming
>>> is incorrect. Firstly I believe the residue name should be PPC for the
>>> entire lipid. If you run leap and load PPC.lib and then edit PPC you can
>>> choose to turn on the atom names in the menu and you'll be able to see
>>> what atom names leap expects.
>>>
>>>
>>> All the best
>>> Ross
>>>
>>> On 11/13/12 2:18 AM, "Albert" <mailmd2011.gmail.com> wrote:
>>>
>>>> hello:
>>>>
>>>> I am using the following command to generate a membrane system for
>>>> POPC GAFF:
>>>>
>>>> tleap -s -f leaprc.ff12SB
>>>>
>>>> source leaprc.gaff
>>>> source GAFFlipid.dat
>>>> loadamberparams GAFFlipid.frcmod
>>>> loadoff PPC.lib
>>>> loadamberparams ligand.frcmod
>>>> loadoff ligand.lib
>>>>
>>>> mol = loadpdb g2a.pdb
>>>> saveamberparm mol sys.prmtop sys.inpcrd
>>>>
>>>>
>>>> but it said:
>>>>
>>>> FATAL: Atom .R<OL 997>.A<C18 19> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H8R 20> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H8S 21> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<C19 22> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H9R 23> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<C110 24> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H10R 25> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<C111 26> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H11R 27> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H11S 28> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<C112 29> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H12R 30> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H12S 31> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<C113 32> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H13R 33> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H13S 34> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<C114 35> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H14R 36> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H14S 37> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<C115 38> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H15R 39> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H15S 40> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<C116 41> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H16R 42> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H16S 43> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<C117 44> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H17R 45> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H17S 46> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<C118 47> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H18R 48> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H18S 49> does not have a type.
>>>> FATAL: Atom .R<OL 997>.A<H18T 50> does not have a type.
>>>>
>>>>
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Received on Wed Nov 14 2012 - 01:30:02 PST
