Dear all,
I try to perform MD simulaiton for a nano-scale molecule. This molecule is composed of many repeating unit with P atoms. I want to build its parameters through the gaff force field. I tried three methods but all failed:
1. Directly use antechamber to calculate the relevant parameters. This molecule contains about 400 atoms. It may be due to too many atoms. After calculation, it shows:
"Info: the bond number exceeds the MAXBOND, reallocate memory, automatically
Info: the actual number of rings (28540) exceeds the defaut ring size (500), reallocate memory automatically** Error ** : realloc() failed"
The calculation suffers error.
2. Directly read the gaff force field and assign the P atom to the p3 atom type of the gaff force field. The PDB content is as follows:
"ATOM 1 P1 MOL 2 0.353 0.000 2.131 1.00 0.01 P
ATOM 2 P2 MOL 2 2.543 1.658 0.000 1.00 0.01 P
ATOM 3 P3 MOL 2 1.836 1.658 2.131 1.00 0.01 P
ATOM 4 P4 MOL 2 4.026 0.000 0.000 1.00 0.01 P
ATOM 5 P5 MOL 2 4.733 0.000 2.131 1.00 0.01 P
ATOM 6 P6 MOL 2 6.922 1.658 0.000 1.00 0.01 P
ATOM 7 P7 MOL 2 6.216 1.658 2.131 1.00 0.01 P
ATOM 8 P8 MOL 2 8.405 0.000 0.000 1.00 0.01 P
ATOM 9 P9 MOL 2 9.112 0.000 2.131 1.00 0.01 P
ATOM 10 P10 MOL 2 11.302 1.658 0.000 1.00 0.01 P
ATOM 11 P11 MOL 2 10.595 1.658 2.131 1.00 0.01 P
ATOM 12 P12 MOL 2 12.785 0.000 0.000 1.00 0.01 P
ATOM 13 P13 MOL 2 13.491 0.000 2.131 1.00 0.01 P
...... Ħħ
My approach is as follows:
Edit a shell script:
for ((i=1;i<=240;i=i+1))
do
echo "set a.2.$i type p3" >> leapdo
done
This script generate a leapdo file, then enter tleap:
"source leaprc.gaff
a = loadpdb nano.pdb
bondbydistance a
source leapdo"
But the result is still an error, the information is as follows:
"> source leapdo
----- Source: ./leapdo
----- Source of ./leapdo done
a.2.1: not a container (e.g. residue)
Usage: set <container> <parameter> <object>
Or: set default <parameter> <value>
a.2.2: not a container (e.g. residue)
Usage: set <container> <parameter> <object>
Or: set default <parameter> <value>
a.2.3: not a container (e.g. residue)
Usage: set <container> <parameter> <object>
Or: set default <parameter> <value>
a.2.4: not a container (e.g. residue)
Usage: set <container> <parameter> <object>
Or: set default <parameter> <value>
......Ħħ
So what is the wrong step?
3. Finally, I tried another method. I first generate the force field parameters for a unit. And then generate the parameters for the entire molecule. However, in this process, there is only bond relationship inside the unit. And there is no bond relationship between the unit and the unit. In addition, the atomic type generated by the antechamber does not conform to the actual molecule. For example, if there is only one unit, then antechamber will automatically determine the double bond and specify the atom type as p2.
For example, the information of a unit is as follows:
"ATOM 1 P1 MOL 2 0.353 0.000 2.131 1.00 0.01 P
ATOM 2 P3 MOL 2 2.543 1.658 0.000 1.00 0.01 P
ATOM 3 P2 MOL 2 1.836 1.658 2.131 1.00 0.01 P
ATOM 4 P4 MOL 2 4.026 0.000 0.000 1.00 0.01 P
TER
END"
The overall molecular is as follows:
"ATOM 1 P1 MOL 1 0.353 0.000 2.131 1.00 0.00
ATOM 2 P3 MOL 1 2.543 1.658 0.000 1.00 0.00
ATOM 3 P2 MOL 1 1.836 1.658 2.131 1.00 0.00
ATOM 4 P4 MOL 1 4.026 0.000 0.000 1.00 0.00
TER
ATOM 5 P1 MOL 2 4.733 0.000 2.131 1.00 0.00
ATOM 6 P3 MOL 2 6.922 1.658 0.000 1.00 0.00
ATOM 7 P2 MOL 2 6.216 1.658 2.131 1.00 0.00
ATOM 8 P4 MOL 2 8.405 0.000 0.000 1.00 0.00
TER
ATOM 9 P1 MOL 3 9.112 0.000 2.131 1.00 0.00
ATOM 10 P3 MOL 3 11.302 1.658 0.000 1.00 0.00
ATOM 11 P2 MOL 3 10.595 1.658 2.131 1.00 0.00
ATOM 12 P4 MOL 3 12.785 0.000 0.000 1.00 0.00
TER
...... Ħħ
If there are many units, how can I link the units into one numerator and generate the overall parameters after generating the parameter file for each unit?
Is there a better way to generate the correct prmtop file and inpcrd file?
Many thanks.
Qiao Xue
xmgign.126.com
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Received on Sun May 26 2019 - 23:30:02 PDT
