I am new to amber any trying to use xleap to make a tetrapeptide tuftsin. After solvation with TIP3PBox 14.0 iso, when I try to save the inpcrd and prmtop file using command
saveamberparm foo tuftsin.inpcrd tuftsin.prmtop
it gives following message
Checking Unit.
WARNING: There is a bond of 3.610664 angstroms between:
------- .R.A and .R.A
WARNING: There is a bond of 4.162462 angstroms between:
------- .R.A and .R.A
WARNING: The unperturbed charge of the unit: 2.000000 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 11 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CARG 1
I am not getting how to solve this error message.
You should remove the water molecules in the original pdb before proceeding and add ions to neutralize the system.
there is no water; I generated pdb in xleap. still I am unable to save parameters by this command
saveamberparm protein peptide.prmtop peptide.inpcrd after adding of ions
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