Dear Mailing List...
I have several problems getting single residue energies out of a system.
I tried around for a time with various suggestions from the web/mailing list, to no avail.
I have two basic problem:
1. I get no vdw and eel
2. the RRES/ LRES does not work
3. can I do something like GB (i come to understand I maybe need this ;-), but with 3-4 internal waters
First, problem 1.
Here is what I want to do:
My trajectory is a 227 AA protein with internal waters run in explicit solvent, with the following
.in:
&cntrl
imin=0,
irest=1,
ntx=5,
nstlim=5000000,
dt=0.002,
ntc=2,
ntf=2,
cut=8.0,
ntb=2,
ntp=1,
taup=2.0,
ntpr=100,
ntwr=1000,
ntwx=1000,
ntt=3,
gamma_ln=2.0,
temp0=300.0,
/
>From this trajectory I want to get single residue energies. NO ligand or something.
After some suggestions I understand that I need "imin = 5" with "-y MYTRAJECTOTY.mdcrd" in the commandline.
If I try:
&cntrl
imin = 5,
idecomp = 1,
maxcyc = 0,
ntmin = 2
ntc=1,
ntf=1,
ntb = 2,
ntp=1,
cut = 8,
ntt=3,
gamma_ln=2.0,
temp0=300.0,
/
Protein
RRES 1 227
END
Nochmal
LRES 1 227
END
Printing
RES 1 227
END
END
My output is:
PRINT DECOMP - TOTAL ENERGIES
resid |internal |vdw |eel |pol |sas
============================================================
TDC 1 19.398 0.000 0.000 0.000 0.000
.....
>From reading I figured out, that this idecomp does not work properly wit ntb > 0 and I better should
strip my molecule of all waters and ions and do igb > 0. Correct?
So I tried the approach from /test:
#decompose energy on a per-residue basis on the trajectory
&cntrl
imin = 5, igb = 5, gbsa = 2,
ntx = 1, maxcyc = 1,
ntc = 1, ntf = 3,
ntb = 0, ntp = 0,
ntwe = 0, ntpr = 500, ntwx=1,
cut = 1000.0, idecomp = 1,
/
Residues considered as REC
RRES 1 227
END
Residues considered as LIG
LRES 1 227
END
Residues to print
RES 1 227
END
END
With a stripped molecule and .prmtop I get:
FATAL: NATOM mismatch in coord and topology files
Is there a trick to go round this problem. I tried to produce the new - water free - .prmtop with tleap on the original .pdb
But obviously i doesnt work... but ok, I will figure out this.
Second and Third Problem can be easily explained on this basis. 2. Even with the RRES/LRES/RES from the /test file, I got:
LOADING THE DECOMP ATOMS AS GROUPS
----- READING GROUP 1; TITLE:
Residues considered as REC
Number of atoms in this group = 0
----- READING GROUP 2; TITLE:
Residues considered as LIG
Number of atoms in this group = 0
----- READING GROUP 3; TITLE:
Residues to print
GRP 3 RES 1 TO 227
Number of atoms in this group = 3541
So LRES and RRES don´t work. Why is that.
Question 3. Some internal waters are important I guess, can I combine igb and a stripped molecule with some internal waters?
Some many questions.... thanks so much!
cheers
André
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Received on Mon Oct 08 2012 - 10:00:03 PDT
