Re: [AMBER] Can we load rst files in leap?

From: Baptiste Legrand <>
Date: Thu, 13 Jan 2011 14:53:25 +0100

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?


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<>wrote:
>> Thanks Jason and Bill for your reply.
>> This is my '' 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 - 06:00:04 PST
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