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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>>>
>>
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Received on Thu Jan 13 2011 - 06:30:04 PST
