Hi Ayesha，
I had noticed that these errors were belonged to the hydrogen atom type
which amber couldn’t recognize well. You should try to delete the hydrogen
atoms from the receptor pdb file. Then, with tleap, build them again. Amber
will automatically added these missing hydrogen atoms.
Best wishes!
Ning
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On 08/18/2020 04:23, [2]Ayesha Fatima wrote:
Good day everyone,
I am trying to prepare my complex on amber18. i prepared my ligand in RED
server and successfully prepared the prmtop and rst files. when I want to
prepare the complex, it gives errors for the protein.
..................................
FATAL: Atom .R<CASP 615>.A<HN 14> does not have a type.
FATAL: Atom .R<ALA 614>.A<HN 11> does not have a type.
FATAL: Atom .R<TYR 613>.A<HN 22> does not have a type.
FATAL: Atom .R<SER 611>.A<HN 12> does not have a type.
FATAL: Atom .R<TRP 610>.A<HN 25> does not have a type.
FATAL: Atom .R<ASP 609>.A<HN 13> does not have a type.
FATAL: Atom .R<THR 608>.A<HN 15> does not have a type.
FATAL: Atom .R<SER 607>.A<HN 12> does not have a type.
FATAL: Atom .R<TRP 606>.A<HN 25> does not have a type.
FATAL: Atom .R<GLY 605>.A<HN 8> does not have a type.
FATAL: Atom .R<VAL 604>.A<HN 17> does not have a type.
FATAL: Atom .R<PHE 603>.A<HN 21> does not have a type.
FATAL: Atom .R<SER 602>.A<HN 12> does not have a type.
FATAL: Atom .R<ASN 601>.A<HN 15> does not have a type.
FATAL: Atom .R<LYS 600>.A<HN 23> does not have a type.
FATAL: Atom .R<ASN 599>.A<HN 15> does not have a type.
FATAL: Atom .R<GLN 598>.A<HN 18> does not have a type.
FATAL: Atom .R<ASP 597>.A<HN 13> does not have a type.
.....................................
Prior to this I used the propka server to detect the protonation states
for
HIS. the output .pqr has funny atoms like
ATOM 23 HG22 THR 20 90.084 66.680 49.259 0.0642 1.4870
ATOM 24 HG21 THR 20 89.664 66.662 47.680 0.0642 1.4870
ATOM 25 HB THR 20 90.620 68.783 48.034 0.0043 1.3870
ATOM 26 HG23 THR 20 91.022 65.897 48.173 0.0642 1.4870
......................
Can anyone kindly lead me to any tutorial or a general protocol to resolve
these issues or prepare protein-ligand complexes for AMBER 18. Last time I
used AMBER in 2017.Looks now, I am kind of lost.
I am using WSL with Ubuntu18.0 on windows 10 machine. Hence, I dont have
xleap
Thank you
Regards
Ayesha
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Received on Mon Aug 17 2020 - 20:30:02 PDT
