Dear all,
I want to perform a Thermodynamics integration calculation for calculating
the base pair mutation. The mutation is over a dsDNA with sequence 5'AGGT
*C*A3' 5'T*G*ACCT3' (order of nucleotides as in the pdb) to a sequence
5'AGGT*A*A3' 5'T*T*ACCT3'. The mutation envolve convert the residues 5 and
8 (C and G in the direct and reverse sense) to 17 and 20 (C and G in the
direct and reverse sense). I have performed three different tries using
timerge:
1) > tiMerge :1-12 :13-24 :5,8 :17,20
Using parm dna_solv.parm7
Merging molecules [:1-12] [:13-24] with sc mask [:5,8] [:17,20]
AmberWarning: Molecule atoms are not contiguous! I am attempting to reorder
the atoms to fix this.
Action tiMerge failed
TiMergeError: Cannot have dihedral cross through softcore region. (DIHED :
258 257 254 255). Usually this means you have defined the softcore region
in a way that breaks a ring. Try redefining your softcore region to include
the ring or at least three consecutive atoms.
2) > tiMerge :1-12 :13-24 :5-8 :17-20 :5,8 :17,20 tol 0.1 parm 0
Using parm dna_solv.parm7
Merging molecules [:1-12] [:13-24] with sc mask [:5-8] [:17-20]
Action tiMerge failed
TiMergeError: The number of nonsoftcore atoms in mol1mask and mol2mask must
be the same.
3) > tiMerge :1-12 :13-24 :5 :17 :8 :20
Merging molecules [:1-12] [:13-24] with sc mask [:5] [:17]
Action tiMerge failed
TiMergeError: The number of nonsoftcore atoms in mol1mask and mol2mask must
be the same.
In summary, there is a way make a dual-topology using timerge for a base
pair mutation?
Thanks in advanced
Gabriel
--
Dr. Gabriel E. Jara
Laboatório Nacional de Biociências - CNPEM
Rua Giuseppe Máximo Scolfaro, 10.000
Polo II de Alta Tecnologia de Campinas - Campinas/SP, Brasil
CEP 13083-970, Campinas - SP
Phone: +55 19 3512-1244 - Fax: +55 19 3512-1006
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Received on Thu Mar 12 2020 - 10:30:02 PDT
