Dears:
Now I wanted to do MD simulation for A and B mixed solution. When I use Tleap to generate input files. I have the following problems:
(a) When I act the A and B as a unit, the tleap1.in files is like this:
source oldff/leaprc.ff99SB
source leaprc.gaff2
mol= loadmol2 avmocntf2_monomer-a1.mol2
check mol
loadamberparams avmocntf2_monomer-a1.frcmod
solvent = copy mol1
solvateBox mol solvent 20
savepdb mol avmocntf2_monomer-a1.pdb
saveamberparm mol avmocntf2_monomer-a1.prmtop avmocntf2_monomer-a1.inpcrd
quit
In this situation, I can correctly generate inputfiles but when I do first step optimization, the job was terminated with 'Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM.' I have check the total natoms is equal in prmtop and inpcrd files. Why?
(b) When I act the A and B as separated, the tleap2.in files is like this:
source oldff/leaprc.ff99SB
source leaprc.gaff2
mol1= loadmol2 avmocntf2_monomer-a1_a.mol2
check mol1
loadamberparams avmocntf2_monomer-a1_a.frcmod
mol2= loadmol2 avmocntf2_monomer-a1_b.mol2
check mol2
loadamberparams avmocntf2_monomer-a1_b.frcmod
set mol1 tail mol1.1.H1
set mol2 head mol2.1.O1
desc mol2
desc mol1
mol=sequence{mol1,mol2}
solvent = copy mol
solvateBox mol solvent 20
savepdb mol avmocntf2_monomer-a1.pdb
saveamberparm mol avmocntf2_monomer-a1.prmtop avmocntf2_monomer-a1.inpcrd
quit
In this situation, the total charge of the mixed solution was not equal to zero for the number of A and B are nor equal (A is Positive charged and B is negative charged),Why?
How can I correctly generate inputfiles for MD simulatioA nad B mixed solution (with same number A and B).
See the attached for related documents.
Thanks very much!
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- application/octet-stream attachment: tleap1.in
- application/octet-stream attachment: tleap2.in
Received on Wed Nov 01 2017 - 19:00:02 PDT
