Hi amber
First of all, the protein which i have taken is taken from the RCSB database. And I have also neutralized the system, adding Na+ ions, as suggested by Stefano. But the total energies are still comming positive. Can somebody help me in finding the exact problem.
Bye
Stefano.Pieraccini.unimi.it wrote:
I notice, on the attached output, that you haven't neutralized the sistem. A neutral sistem is required for ewald sum, and it is artificially neutralized with uniform plasma (see your output). Maybe this can cause a problem. You problem could also depend on the initial structure. If it is a PDB file or a part of a pdb file, there should be no problems, but if it was drawn by hand, some artifacts may be present that make the energy high and that can't be solved by minimization.
Stefano Pieraccini
Content-type: multipart/alternative;
boundary="Boundary_(ID_oOhDSNnNENFnNM4uD5RcJQ)"
--Boundary_(ID_oOhDSNnNENFnNM4uD5RcJQ)
Content-type: text/plain; charset=us-ascii
Content-transfer-encoding: 7BIT
hello amber,
I am performing Implicit solvent md on small proteins using 4r dielectric, restraing the helices ans sheets. The input file for the initial minimization step is:
&cntrl
imin=1,
ntx=1,ntb=0,
ntr=1,dielc=4,cut=300.0,
maxcyc=1000, ncyc=500,
&end
&ewald
eedmeth=5,
&end
restraint 1
25.0
RES 10 19
RES 25 37
RES 42 55
END
END
My problem is that the total energy at the start of the minimization is positive and after the minimization (1000 steps) is positive. Is there someting which i am doing wrong, because of which total energy is positive. I am attaching the output file.
Thanks.
---------------------------------
Do you Yahoo!?
Take Yahoo! Mail with you! Get it on your mobile phone.
--Boundary_(ID_oOhDSNnNENFnNM4uD5RcJQ)
Content-type: text/html; charset=us-ascii
Content-transfer-encoding: 7BIT
hello amber,
I am performing Implicit solvent md on small proteins using 4r dielectric, restraing the helices ans sheets. The input file for the initial minimization step is:
&cntrl
imin=1,
ntx=1,ntb=0,
ntr=1,dielc=4,cut=300.0,
maxcyc=1000, ncyc=500,
&end
&ewald
eedmeth=5,
&end
restraint 1
25.0
RES 10 19
RES 25 37
RES 42 55
END
END
My problem is that the total energy at the start of the minimization is positive and after the minimization (1000 steps) is positive. Is there someting which i am doing wrong, because of which total energy is positive. I am attaching the output file.
Thanks.
---------------------------------
Do you Yahoo!?
Take Yahoo! Mail with you! Get it on your mobile phone.
--Boundary_(ID_oOhDSNnNENFnNM4uD5RcJQ)--
---------------------------------
Do you Yahoo!?
Dress up your holiday email, Hollywood style. Learn more.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Dec 03 2004 - 05:53:01 PST
