[AMBER] How to generate inpcrd and prmtop files for A and B mixed solution

From: <ymy0664.163.com>
Date: Thu, 2 Nov 2017 09:52:38 +0800 (CST)

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!










_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed Nov 01 2017 - 19:00:02 PDT
Custom Search