Hi,
Thanks for your answer.
I am using Amber coordinates option when i load the mdcrd file .
Otherwise i have 2000 frames in the trajectory. but when i download the ptraj result file "MD_PC_NoWat_test.mdcrd" i've got 398 frames while i am suppose to obtain only 10 frames using "trajin 2AHI_MD1.mdcrd 1 9999999999 100".
All the best,
OZ
________________________________________
From: Sangita Kachhap [sangita.imtech.res.in]
Sent: Sunday, October 16, 2011 3:21 PM
To: AMBER Mailing List
Subject: Re: [AMBER] SASA calculation: removing water and ion problem.
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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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Received on Sun Oct 16 2011 - 09:30:02 PDT
