Date: Fri, 22 Apr 2022 15:58:11 +0900
Hello Everyone,
Recently I am doing calculations on a polymer system. A schematic
geometry of the polymer (real one has many more monomers and long side
chains) is shown in the attached figure. There monomers are connected by
two bonds and form a spiro linkage. I have optimized and completed
charge calculation and performed the antechamber module. The “leap” gave
me FATAL ERROR as,
/usr/local/anaconda3/envs/AmberTools21/bin/teLeap: Error!
Comparing atoms
.R<H4H 1>.A<C2 1>,
.R<H4H 1>.A<C4 4>,
.R<H4H 1>.A<H1 17>, and
.R<H4H 1>.A<H2 18>
to atoms
.R<H4H 1>.A<C2 1>,
.R<M4H 1>.A<C10 1>,
.R<H4H 1>.A<H1 17>, and
.R<H4H 1>.A<C4 4>
This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [/Users/runner/miniforge3/conda-bld/ambertools_
1645002236808/work/AmberTools/src/leap/src/leap/chirality.c], line 142
!FATAL: Message: Atom named C10 from M4H did not match !
!
!ABORTING.
I have used two HEAD (or TAIL) atoms in some cases. One example (middle
part) is,
HEAD_NAME C21
HEAD_NAME C10
TAIL_NAME C57
OMIT_NAME C11
OMIT_NAME C12
OMIT_NAME H1
OMIT_NAME H2
OMIT_NAME H75
OMIT_NAME C13
OMIT_NAME H76
OMIT_NAME H77
OMIT_NAME H78
OMIT_NAME C56
OMIT_NAME H72
OMIT_NAME H73
OMIT_NAME H82
OMIT_NAME C66
OMIT_NAME H79
OMIT_NAME H80
OMIT_NAME H81
PRE_HEAD_TYPE c3
PRE_HEAD_TYPE c3
POST_TAIL_TYPE ca
POST_TAIL_TYPE c3
CHARGE 0.0
This is also suspecious to me.
If anyone has any suggestions or idea that how to generate force field
for such system? How to add proper connectivity with the head and tail,
where two connectivity is required, while using “prepgen” and “leap”? Is
it possible to connect this problem to the addition of disulfide (
protein) linkage by leap program?
Thank you in advance.
Regards
Ranajit
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