Dear AMBER users,
I'm now working on a MD simulation to an enzyme which has peculiar ligands. Followed the official tutorial which dealing with non-standard residue (link: http://ambermd.org/tutorials/advanced/tutorial1_adv/) I created a new residue "ATP" which contains an ATP as well as a magnesium ion (nominated as "MG" and it does not exist in the library).
The template of the new residue was first generated by Gaussian 09 (by single point charge calculation), then use "antechamber" in AMBER to shift it into ".mol2" format, which contains atom charges and connection information, etc. A ".frcmod" file was created simultaneously, said that the MASS and NONBON parameters of MG should be revised. MASS was pretty easy to obtain, NONBON was directly use those original information in AMBER lib.
In "tleap", the residue I manually created was imported directly by the command "loadmol2". The final model for simulation was then successfully generated. The minimization step was OK, using 5000 step of SD method as well as 5000 step of CONJ method without restriction to the protein. Issue occurred when it came to the starting point of heating step:
(the last lines in the output file)
vlimit exceeded for step 3; vmax = 21.5763
vlimit exceeded for step 4; vmax = 115.6802
vlimit exceeded for step 5; vmax = 221.8382
vlimit exceeded for step 6; vmax = 74.7778
vlimit exceeded for step 7; vmax = 42.8791
Here are the ".frcmod" file and my MD input condition:
(.frcmod file)
------------------------------------------------
remark goes here
MASS
MG 24.305
BOND
ANGLE
DIHE
IMPROPER
c3-ca-na-cc 1.1 180.0 2.0 Using default value
h5-na-cc-nd 1.1 180.0 2.0 Using default value
ca-ca-ca-nd 1.1 180.0 2.0 Using default value
ca-nb-ca-nh 1.1 180.0 2.0 Using default value
ca-hn-nh-hn 1.1 180.0 2.0 Using default value
h5-nb-ca-nb 1.1 180.0 2.0 Using default value
ca-na-ca-nb 1.1 180.0 2.0 Using default value
NONBON
MG 0.7926 0.8947 ATTN, need revision
------------------------------------------------
(MD input file)
------------------------------------------------
Heating
&cntrl
imin=0,irest=0,ntx=1,ntb=1,
cut=10.0,ntr=1,restraint_wt=0.5,restraintmask=':1-395',
ntc=2,ntf=2,
tempi=0.0,temp0=300.0,
ntt=1,nstlim=50000,dt=0.001,ntpr=100,ntwx=100,ntwr=200
I'm pretty appreciated if anyone could help me to get through that issue.
P.S. In my previous work, I utilized the normal template which exist in the AMBER lib (name: MG2) for the magnesium ion. The template of ATP did not contain the magnesium ion. The ".frcmod" file corresponding to ATP was just as the one I provided above, but without information on MG. Everything went fine from minimization to heating, equilibration and MD simulation with NPT ensemble. Hopefully what I mention here make sense.
Many thanks,
Xiaozhou
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 13 2011 - 06:30:03 PST
