[AMBER] Query about protein DNA MD

From: Vikram Dalal <vikram.dalal.37.gmail.com>
Date: Fri, 8 Mar 2019 22:59:34 +0530

Dear All,


I have done this in tleap:-


protein.ff14SB
DNA.OL15



PDB file has protein and DNA coordinate separated by TER card.

Still, I am getting this error in tleap:-

FATAL: Atom .R<DT 110>.A<H3T 33> does not have a type.
FATAL: Atom .R<DA 111>.A<H5T 33> does not have a type.
FATAL: Atom .R<NGLU 126>.A<HN 18> does not have a type.
FATAL: Atom .R<ARG 127>.A<HN 25> does not have a type.
FATAL: Atom .R<CYS 128>.A<HN 12> does not have a type.
FATAL: Atom .R<ARG 129>.A<HN 25> does not have a type.
FATAL: Atom .R<GLN 130>.A<HN 18> does not have a type.
FATAL: Atom .R<MET 131>.A<HN 18> does not have a type.
FATAL: Atom .R<SER 132>.A<HN 12> does not have a type.
FATAL: Atom .R<ALA 133>.A<HN 11> does not have a type.
FATAL: Atom .R<ARG 134>.A<HN 25> does not have a type.
FATAL: Atom .R<GLU 135>.A<HN 16> does not have a type.
FATAL: Atom .R<GLU 136>.A<HN 16> does not have a type.
FATAL: Atom .R<LEU 137>.A<HN 20> does not have a type.
FATAL: Atom .R<ARG 138>.A<HN 25> does not have a type.
FATAL: Atom .R<SER 139>.A<HN 12> does not have a type.
FATAL: Atom .R<CYS 140>.A<HN 12> does not have a type.
FATAL: Atom .R<GLU 141>.A<HN 16> does not have a type.
FATAL: Atom .R<GLN 142>.A<HN 18> does not have a type.
FATAL: Atom .R<TYR 143>.A<HN 22> does not have a type.
FATAL: Atom .R<LEU 144>.A<HN 20> does not have a type.
FATAL: Atom .R<ARG 145>.A<HN 25> does not have a type.
FATAL: Atom .R<GLN 146>.A<HN 18> does not have a type.
FATAL: Atom .R<GLN 147>.A<HN 18> does not have a type.
FATAL: Atom .R<SER 148>.A<HN 12> does not have a type.
FATAL: Atom .R<ARG 149>.A<HN 25> does not have a type.
FATAL: Atom .R<GLU 150>.A<HN 16> does not have a type.
FATAL: Atom .R<VAL 151>.A<HN 17> does not have a type.
FATAL: Atom .R<LEU 152>.A<HN 20> does not have a type.
FATAL: Atom .R<GLN 153>.A<HN 18> does not have a type.
FATAL: Atom .R<MET 154>.A<HN 18> does not have a type.
FATAL: Atom .R<ARG 155>.A<HN 25> does not have a type.
FATAL: Atom .R<GLY 156>.A<HN 8> does not have a type.
FATAL: Atom .R<ILE 157>.A<HN 20> does not have a type.
FATAL: Atom .R<GLU 158>.A<HN 16> does not have a type.
FATAL: Atom .R<ASN 159>.A<HN 15> does not have a type.
FATAL: Atom .R<TRP 161>.A<HN 25> does not have a type.
FATAL: Atom .R<ARG 162>.A<HN 25> does not have a type.
FATAL: Atom .R<ARG 163>.A<HN 25> does not have a type.








Thanks & Regards,










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