[AMBER] Dimension Box visualization

From: Aashish Bhatt <aashish.ph16221.inst.ac.in>
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:

>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

What could be the issue and how can i rectify it?

Best Regards
Aashish Bhatt

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Received on Wed May 30 2018 - 23:30:02 PDT
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