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

From: Baptiste Legrand <>
Date: Thu, 13 Jan 2011 10:15:25 +0100

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 - 01:30:03 PST
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