Dear AmberExperts,
i am stuck in a problem. i am trying to generate topology and
coordinate files for a a protein-DNA complex. i have incorporated an
adduct in the DNA and made a point mutation in the protein. i am not
able to generate the prmtop and inpcrd files for my complex. here i am
pasting the error i am getting as well as my leap.in file. the frcmod
and mol2 files are correct i hope because i have used them successfully
in a previous complex. what could be the possible error in this? MOL is
the modified nucleobase. IN2 is the incoming nucleotide in my system.
Building topology.
Building atom parameters.
Error: For atom (.R<MOL 351>.A<P1 1>) could not find vdW (or other)
parameters for type (p4)
Error: For atom (.R<MOL 351>.A<O1 2>) could not find vdW (or other)
parameters for type (o)
Error: For atom (.R<MOL 351>.A<O2 3>) could not find vdW (or other)
parameters for type (o)
Error: For atom (.R<MOL 351>.A<O3 4>) could not find vdW (or other)
parameters for type (os)
Error: For atom (.R<MOL 351>.A<C1 5>) could not find vdW (or other)
parameters for type (c3)
Error: For atom (.R<MOL 351>.A<H1 6>) could not find vdW (or other)
parameters for type (h1)
Error: For atom (.R<MOL 351>.A<H2 7>) could not find vdW (or other)
parameters for type (h1)
Error: For atom (.R<MOL 351>.A<C2 8>) could not find vdW (or other)
parameters for type (c3)
Error: For atom (.R<MOL 351>.A<H3 9>) could not find vdW (or other)
parameters for type (h1)
Error: For atom (.R<MOL 351>.A<O4 10>) could not find vdW (or other)
parameters for type (os)
Error: For atom (.R<MOL 351>.A<C3 11>) could not find vdW (or other)
parameters for type (c3)
Error: For atom (.R<MOL 351>.A<H4 12>) could not find vdW (or other)
parameters for type (h2)
Error: For atom (.R<MOL 351>.A<N1 13>) could not find vdW (or other)
parameters for type (na)
Error: For atom (.R<MOL 351>.A<C4 14>) could not find vdW (or other)
parameters for type (cc)
Error: For atom (.R<MOL 351>.A<H5 15>) could not find vdW (or other)
parameters for type (h5)
Error: For atom (.R<MOL 351>.A<N2 16>) could not find vdW (or other)
parameters for type (nd)
Error: For atom (.R<MOL 351>.A<C5 17>) could not find vdW (or other)
parameters for type (cd)
Error: For atom (.R<MOL 351>.A<C6 18>) could not find vdW (or other)
parameters for type (c)
Error: For atom (.R<MOL 351>.A<O5 19>) could not find vdW (or other)
parameters for type (o)
Error: For atom (.R<MOL 351>.A<N3 20>) could not find vdW (or other)
parameters for type (n)
Error: For atom (.R<MOL 351>.A<H6 21>) could not find vdW (or other)
parameters for type (hn)
Error: For atom (.R<MOL 351>.A<C7 22>) could not find vdW (or other)
parameters for type (cd)
Error: For atom (.R<MOL 351>.A<N4 23>) could not find vdW (or other)
parameters for type (nh)
Error: For atom (.R<MOL 351>.A<H7 24>) could not find vdW (or other)
parameters for type (hn)
Error: For atom (.R<MOL 351>.A<N5 25>) could not find vdW (or other)
parameters for type (nc)
Error: For atom (.R<MOL 351>.A<C8 26>) could not find vdW (or other)
parameters for type (cc)
Error: For atom (.R<MOL 351>.A<C9 27>) could not find vdW (or other)
parameters for type (c3)
Error: For atom (.R<MOL 351>.A<H8 28>) could not find vdW (or other)
parameters for type (h1)
Error: For atom (.R<MOL 351>.A<C10 29>) could not find vdW (or other)
parameters for type (c3)
Error: For atom (.R<MOL 351>.A<H9 30>) could not find vdW (or other)
parameters for type (hc)
Error: For atom (.R<MOL 351>.A<H10 31>) could not find vdW (or other)
parameters for type (hc)
Error: For atom (.R<MOL 351>.A<O6 32>) could not find vdW (or other)
parameters for type (o)
Error: For atom (.R<MOL 351>.A<C11 33>) could not find vdW (or other)
parameters for type (c3)
Error: For atom (.R<MOL 351>.A<C12 34>) could not find vdW (or other)
parameters for type (c3)
Error: For atom (.R<MOL 351>.A<H11 35>) could not find vdW (or other)
parameters for type (h1)
Error: For atom (.R<MOL 351>.A<H12 36>) could not find vdW (or other)
parameters for type (h1)
Error: For atom (.R<MOL 351>.A<H13 37>) could not find vdW (or other)
parameters for type (hc)
Error: For atom (.R<MOL 351>.A<H14 38>) could not find vdW (or other)
parameters for type (hc)
Error: For atom (.R<MOL 351>.A<H15 39>) could not find vdW (or other)
parameters for type (hc)
Warning: Parameter file was not saved.
>
my input files is:
source leaprc.protein.ff14SB
source leaprc.DNA.bsc1
source leaprc.water.tip3p
IN2 = loadmol2 IN2.mol2
loadamberparams IN2.frcmod
MOL = loadmol2 N2-Ethyl-fit.mol2
loadamberparams N2-Ethyl-fit.frcmod
unit = loadpdb complex2.pdb
savepdb unit mod.pdb
addions unit Na+ 0
solvatebox unit TIP3PBOX 10.0
saveamberparm unit mod.prmtop mod.inpcrd
savepdb modsol2.pdb
quit
regards,
Priyasha
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Received on Mon Jul 17 2023 - 00:30:02 PDT
