Soroush Ziaei

11 Questions 24 Answers 0 Followers

Questions related from Soroush Ziaei

What is the difference between normal cell membrane & cancerous cell membrane?

for example, I have used POPE cell membrane in my research work (molecular dynamics), but according to the paper that I attached below, this membrane is a kind of normal membrane. if there is...

06 June 2019 3,461 9 View

Hi NAMD users, I have an error that I described below... please tell me what should I do?

recently, I encountered an error at the beginning of the simulation, which related to Atom 3662, please let me know the solution of this error: FATAL ERROR: Atom 3662 has bad hydrogen group size. ...

05 May 2019 7,983 3 View

How to create topology for a unique structure?

i have some structure that doesn't have any similar topology in charmm22 (protein) & charmm 27 (lipid) and i have tried several servers such as, cgenff & swiss param, but the .rtf file...

11 November 2018 8,441 3 View

Hi all, please see this error message about namd config file and tell me what should i do to solve that?

# error message: TCL: can't read "temp": no such variable FATAL ERROR: can't read "temp": no such variable while executing "runFEPmin 0.0 0.0 0.0 $numSteps $numMinSteps $temp" (file...

10 October 2018 513 4 View

Hi all, I want to perform calculation of free energy <fep> for a drug in the water box. Is there somebody who can provide me with a input file?

i interested in achieve delta(g) and I have read tutorial for fep but i didn't get useful information about creating input file.

10 October 2018 6,768 9 View

Hi all, does anybody have charmm program?

if someone have this software, I appreciate the one who send it.

02 February 2018 3,645 7 View

Hi all, does anybody know about calculation of solvation free energy?

i tried on charmm-gui site but an error appears, what should i do? is there another way to calculate that?

02 February 2018 9,633 6 View

Hi everybody, i tried to obtain parameter file with cgenff but an error appears. what should i do?

the details of this error is shown below: (readmol2 warning: wildcard atom types not allowed; skipped molecule MOL2), also i tried another method such as swiss param website but i did not receive...

12 December 2017 8,896 4 View

Hi everybody, i want to know how to create parameter file with fftk on vmd, can anybody help me?

after creation initial parameter file, i stuck in second step that require optimization log file, please help me, guys.

12 December 2017 9,663 2 View

Hi everybody, i tried to obtain parameter file with cgenff but an error appears. what should i do?

the details of this error is shown below: (readmol2 warning: wildcard atom types not allowed; skipped molecule MOL2), also i tried another method such as swiss param website but i did not receive...

12 December 2017 5,405 4 View

Hi everybody, i want to know how to create parameter file with fftk on vmd, can anybody help me?

after creation initial parameter file, i stuck in second step that require optimization log file, please help me, guys.

12 December 2017 5,395 4 View