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.
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 13 2012 - 09:30:04 PST
