Hi,
What that means is that MMPBSA doesn't have the parameters for iodine- try
checking
http://archive.ambermd.org/201111/0370.html for a solution, then
recompile Amber in serial.
If you're using AmberTools15, I think it changes to mdread2.F90 that you'll
want to edit around.
Best,
Kenneth
On Sat, Sep 5, 2015 at 12:48 AM, <21428087.zju.edu.cn> wrote:
> Dear ALL:
> I am Peter.Now I have some problems about AMBER. When I run "MMPBSA.py
> -O -i mmpbsa.in -sp comp_wat.prmtop -cp comp.prmtop -rp res.prmtop -lp
> ligand.prmtop -y md1.mdcrd",there's something wrong like:
>
>
>
> "staring gb calculation...
> bad atom type:i
> calculating receptor contribution...
> calculationg complex contribution...
> bad atom type:i"
>
>
> My mmpbsa.in is:
>
>
> "Input file for running PB and GB
> &general
> startframe=34, endframe=50, interval=1, verbose=1,
> /
> &gb
> igb=5, saltcon=0.100
>
>
> &pb
> istrng=0.100,
> /
> #&nmode
> #maxcyc=50000,
> "
> My ligand has Iodine and my ligand.prmtop is in the accessory.
> What could I do for this? Hope for your reply!Thanks!
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
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here could not dream of heaven?
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Received on Sat Sep 05 2015 - 17:30:03 PDT
