Thanks Jason, I'm going to try it.
Le 13/01/2011 15:39, Jason Swails a écrit :
> Yes, you will be able to solvate that structure. You should still relax and
> heat the system slowly, then equilibrate it so that the waters settle down.
>
> On Thu, Jan 13, 2011 at 9:19 AM, Baptiste Legrand<bap.legrand.gmail.com>wrote:
>
>> I load the prepin from my sirius file and the pdb resulting from my MD
>> in vacuum and then I will have the structure from my MD in vacuum but
>> solvated and ready for a new MD simulations?
>>
>> Le 13/01/2011 15:09, Jason Swails a écrit :
>>> That shouldn't be necessary -- just load the prepin file you have from
>> last
>>> time
>>>
>>> On Thu, Jan 13, 2011 at 8:53 AM, Baptiste Legrand<bap.legrand.gmail.com
>>> wrote:
>>>
>>>> I have created a pdb/mol2 template file using sirius and then I have
>>>> run antechamber before starting a MD in vacuum. So I have just the
>>>> initial prepin file and the corresponding prmtop and inpcrd.
>>>> Perhaps, a solution may be to create a pdb from my final rst file and
>>>> then to launch a second time antechamber to have the prepin from this
>>>> file (with the good coordinates) before the MD in explicit solvent?
>>>>
>>>> Baptiste
>>>>
>>>> Le 13/01/2011 14:31, Jason Swails a écrit :
>>>>> Did you not have an amber prep or OFF library file for residue UNK when
>>>> you
>>>>> first created the topology file? It's these library files that
>> provides
>>>> the
>>>>> atom name -> atom type mapping needed here.
>>>>>
>>>>> Good luck,
>>>>> Jason
>>>>>
>>>>> On Thu, Jan 13, 2011 at 4:15 AM, Baptiste Legrand<
>> bap.legrand.gmail.com
>>>>> wrote:
>>>>>
>>>>>> Thanks Jason and Bill for your reply.
>>>>>> This is my 'leap.in' file:
>>>>>> source leaprc.gaff
>>>>>> source leaprc.ff99SB
>>>>>> UNK=loadpdb sa2_ct_12.pdb
>>>>>> loadamberparams sa2_ct_12.frcmod
>>>>>> solvatebox UNK TIP3PBOX 8 0.75
>>>>>> saveamberparm UNK ./wat/prep/sa2_ct_12.prmtop
>>>> ./wat/prep/sa2_ct_12.inpcrd
>>>>>> And thes errors in the leap.out:
>>>>>> ...
>>>>>> FATAL: Atom .R<UNK 1>.A<H10 85> does not have a type.
>>>>>> FATAL: Atom .R<UNK 1>.A<H26 86> does not have a type.
>>>>>> FATAL: Atom .R<UNK 1>.A<C30 87> does not have a type.
>>>>>> FATAL: Atom .R<UNK 1>.A<H7 88> does not have a type.
>>>>>> FATAL: Atom .R<UNK 1>.A<H19 89> does not have a type.
>>>>>> Failed to generate parameters
>>>>>> Parameter file was not saved.
>>>>>>
>>>>>> The errors may come from the fact that that my peptide is modified and
>>>>>> was generated first by antechamber (for the calculations in vacuum).
>> So,
>>>>>> as the nomenclature is not standard, leap cannot find the atom type
>> for
>>>>>> each atom in its library?
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Le 12/01/2011 20:22, Bill Ross a écrit :
>>>>>>>> I want to use structures from a previous MD run in vacuum to launch
>> a
>>>>>>>> run in a solvent box. Is it possible to load directly my rst and
>>>> prmtop
>>>>>>>> files in leap to create "solvated" starting files?
>>>>>>>> For the moment, I have convert the rst files in pdb using ambpdb
>>>>>>>> nevertheless the generated pdb don't have the 'atom type' column and
>>>>>>>> cannot be loaded in leap.
>>>>>>> You need to use the pdb, loadpdb, solvate, and saveamberparm.
>>>>>>> There is no such thing as an 'atom type' column in pdb that
>>>>>>> leap requires. If you have the same setup as when you generated
>>>>>>> the vacuum saveamberparm, the pdb should load ok. If you send
>>>>>>> whatever error/warning messages you are seeing, we can diagnose
>>>>>>> directly.
>>>>>>>
>>>>>>> Bill
>>>>>>>
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Received on Thu Jan 13 2011 - 09:30:02 PST
