Date: Thu, 31 May 2018 11:30:50 +0530
Dear Sir
I need to perform dynamics for a protein complex. For this i tried making
the topology and coordinate file. When i visualized topology file and pdb
file in VMD, Dimensions of the box are not cubic(attached files).
I used the following commands:
>tleap
>source leaprc.ff14SB.redq
>mol=loadpdb my.pdb
>solvatebox mol TIP3PBOX 15
>addions mol Na+ 202
>addions mol Cl- 202
>saveamberparm mol my_solv.prmtop my_solv.inpcrd
>savepdb mol my_solv.pdb
>quit
What could be the issue and how can i rectify it?
Best Regards
Aashish Bhatt
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