Dear Amber Users,
PROBLEM 1
I am creating force fields of SAM (S-Adenosyl methionine) using
antechamber tutorial 4b. While checking the generated .mol2 file,
tleap returned the following warnings
:" Warning: Close contact of 1.489783 angstroms between .R<SAM
1>.A<HN62 30> and .R<SAM 1>.A<HN61 31>
Warning: Close contact of 1.488686 angstroms between .R<SAM 1>.A<HN2
34> and .R<SAM 1>.A<HN1 35>
Warning: Close contact of 1.460840 angstroms between .R<SAM 1>.A<HG1
37> and .R<SAM 1>.A<H4' 45>" .
Are these warnings serious enough to be considered ??
PROBLEM 2
While creating topology and coordinate files for my required protein
complex using the same above mentioned tutorial, xleap generated the
following statements:
> saveamberparm complex hMT_SAM.prmtop hMT_SAM.inpcrd
Checking Unit.
FATAL: Atom .R<SAM 322>.A<N 1> does not have a type.
FATAL: Atom .R<SAM 322>.A<CA 2> does not have a type.
FATAL: Atom .R<SAM 322>.A<C 3> does not have a type.
FATAL: Atom .R<SAM 322>.A<O 4> does not have a type.
FATAL: Atom .R<SAM 322>.A<CB 5> does not have a type.
FATAL: Atom .R<SAM 322>.A<CG 6> does not have a type.
FATAL: Atom .R<SAM 322>.A<SD 7> does not have a type.
FATAL: Atom .R<SAM 322>.A<CE 8> does not have a type.
FATAL: Atom .R<SAM 322>.A<C5' 9> does not have a type.
FATAL: Atom .R<SAM 322>.A<C4' 10> does not have a type.
FATAL: Atom .R<SAM 322>.A<O4' 11> does not have a type.
FATAL: Atom .R<SAM 322>.A<C3' 12> does not have a type.
FATAL: Atom .R<SAM 322>.A<O3' 13> does not have a type.
FATAL: Atom .R<SAM 322>.A<C2' 14> does not have a type.
FATAL: Atom .R<SAM 322>.A<O2' 15> does not have a type.
FATAL: Atom .R<SAM 322>.A<C1' 16> does not have a type.
FATAL: Atom .R<SAM 322>.A<OXT 17> does not have a type.
FATAL: Atom .R<SAM 322>.A<N1 18> does not have a type.
FATAL: Atom .R<SAM 322>.A<C2 19> does not have a type.
FATAL: Atom .R<SAM 322>.A<N3 20> does not have a type.
FATAL: Atom .R<SAM 322>.A<C4 21> does not have a type.
FATAL: Atom .R<SAM 322>.A<C5 22> does not have a type.
FATAL: Atom .R<SAM 322>.A<C6 23> does not have a type.
FATAL: Atom .R<SAM 322>.A<N6 24> does not have a type.
FATAL: Atom .R<SAM 322>.A<N7 25> does not have a type.
FATAL: Atom .R<SAM 322>.A<C8 26> does not have a type.
FATAL: Atom .R<SAM 322>.A<N9 27> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Please suggest what may be the possible cause of error.
Thanks,
Swithin
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Received on Tue Feb 24 2015 - 11:30:03 PST
