AMBER Archive (2009)

Subject: [AMBER] Some queries about pH simulation

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Thu Oct 08 2009 - 23:36:56 CDT

Dear community,
                        I am trying to simulate my protein in different
different pHs. I using the procedure given in Amber9 manual (page 172-177).
I am facing some problem and in dilemma about am I doing the right
procedure. I am writing the queries and dilemma serial wise.

1. Page 172 of manual when I type the following command in tleap
> loadAmberParams frcmod.mod_phipsi.1
it gives error message
Could not open file frcmod.mod_phipsi.1: not found

2. I am not following what -states flag dose.

3. In the -system flag can we use options other than HEWL. If yes then what
are the options.

4. After preparation of topology, coordinate, cspin ect. files I have run
the MD simulation. I have used the same input file mdin given in
$AMBERHOME/test/cnstph/Run.cnstph. But while running sander I needed the -p
prmtop option while it is not present in Run.cnstph.

5. I have not solvated my protein. I hope it is not needed since constant pH
simulation is done in implicit solvent.

Can anybody please reply to my above querries. Thank you in advance. 

-- 
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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