Hi
Are you using "AMBER coordinates with periodic box" option during loading
stripped trajectory in VMD?
How much total frame you have in trajectory, is it 9999999999?
> Hi,
>
> To perform a SASA calculation on my protein, i tried to remove the Water and
> ions from my MD simulation using Ptraj:
>
> trajin 2AHI_MD1.mdcrd 1 9999999999 100
> strip :WAT
> strip :Cl-
> strip :Na+
> trajout MD_PC_NoWat_test.mdcrd
>
> When i check the result on VMD, there is effectively no more water but the
> protein structure is totally disturbed, as the atoms tried to take the space
> left by the water box.
> As parameter topology file i tried with the one i used during the MD simulation
> (including the water box and ions), but i tried also with one without ion and
> water. Both don't work.
> I checked the 2AHI_MD1.mdcrd file, its not the problem.
> Can somebody let me know what i am doing wrong?
>
> Thanks,
>
> OZ.
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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
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Received on Sun Oct 16 2011 - 07:30:02 PDT
