AMBER Archive (2005)

Subject: AMBER: how can I deal with the puzzle?

From: hj zou (hjzou_at_iris3.simm.ac.cn)
Date: Tue Mar 08 2005 - 21:36:39 CST

Hi, amber community,

        I have two conformations of a protein which have a RMSD of 440 angstrom. I want to transfor from one conformation to another. In the simulation, I am confused that My simulation seems not be right in the process of targeted MD. There are several puzzles in my simulations as follows:
1. Could you tell me the parameters I used in the targeted MD is right?
******************************************************************************
targeted MD
 &cntrl
         imin=0, nstlim=10000, dt=0.0005,
        tempi=300,temp0=300,tautp=0.2,
        ntx=5, ntt=1, npscal=1,
        ntc=2, ntf=2, ntb=2,
        ntp=1,
        ntpr=10, scee=1.2, cut=25,
        igb=0, irest=1, nmropt=1,
        lastist = 3500000,lastrst = 5000000,
        itgtmd=1, tgtrmsd=0.0, tgtmdfrc=0.5,
 &end
 &wt
        TYPE='TGTRMSD', istep1 =1, istep2 = 1000,
        value1 = 441.2, value2 = 440.,
 &end
 .....
 &wt
   type="END",
 &end
 &rst
   iat(1)=0,
 &end
group input- define atoms for targeted md
FIND
CA * * *
N * * *
C * * *
O * * *
H * * *
HA * * *
SEARCH
RES 1 446
END
END
*******************************************************************
2.And In the output file, I found the temperature increased from 300K to 320K during 10000 steps, the whole energy was increased from negative value to positive. is it right?
3.Should I use the Born model(igb=1) for targeted MD?

I am greatly appreciated your reply, and Thank you in advance

Best regards,
=====================================
Jian Zhang
Center for Drug Discovery and Design
Shanghai Institute of Materia Medica
Chinese Academy of Sciences
555 Zu Chong Zhi Road
Shanghai 201203, China
Tel: +86-21-50806600-1201(ext)
E-mail: redsnow_at_mail.shcnc.ac.cn　
        jzhang_at_iris3.simm.ac.cn　　

　　　　　　　　嫖宗
　　　　　　　　redsnow_at_mail.shcnc.ac.cn
　　　　　　　　　　2005-03-08

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