Re: [AMBER] RAMD question (Xiaodong Wu)

From: Charles Lin <charles.lin.silicontx.com>
Date: Fri, 5 Feb 2021 18:59:28 +0000

Oh also, ramdprotmask assuming you're not doing a peptide, you can just make your

ramdproteinmask=":ALA,GLY,SER,THR,LEU,ILE,VAL,ASN,GLN,ARG,HID,HIE,HIP,TRP,PHE,TYR,GLU,ASP,LYS,LYN,PRO,CYS,CYX,MET,ASH,GLH,CYM,HYP",

Essentially ramdprotmask and ramdligmask are used to determine the center of mass of the 2 objects you're using. If I remember correctly the center of mass of ramdprotmask and ramdligmask is set as the equilibrium distance and once the ligand goes at a distance greater than (equilibrium distance + ramdmaskdist), the simulation ends.

Hope that helps,
Charlie


On 2/5/21, 6:39 AM, "Carlos Simmerling" <carlos.simmerling.gmail.com> wrote:


    CAUTION: EXTERNAL EMAIL



    Have you tried sander instead of pmemd?

    On Fri, Feb 5, 2021, 4:20 AM 吴晓东 <18xdwu.stu.edu.cn> wrote:

> Dear all,
> I run RAMD by using Amber 20. And the input file was shown as follow.
> However, in my output file, I can't see any information of "RAMD".(As shown
> in RESULTS) I don't know if my input file is written correctly. In
> addition, when I write keyword "ramdprotmask", the system will remind me
> that "Fortran runtime error: Cannot match namelist object name
> ramdprotmask". These problems make me confused about RAMD. At last, the
> command I used for RAMD is "pmemd.cuda -O -i sander.in6 -o sander.out6 -p
> prmtop -c mdrest5 -r mdrest6 -x mdcrd6".
>
> RAMD input file (sander.in6 file):
>
> Production 10 ns
> &cntrl
> irest=1,ntx=5,
> nstlim=5000000,dt=0.002,
> temp0=300.0,ntt=3,gamma_ln=2.0,
> ntc=2,ntf=2,
> cut=8.0,
> ntpr=1,ntwx=2000,ntwv=0,ntwe=0,ntxo=1,iwrap=1,
> ntb=2,ntp=1,pres0=1.0,taup=1.0,
> ipol=0,igb=0,
> ramdboost=1,ramdmaxdist=12,ramdligmask=":484",
> &end
>
> Output file:
>
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
>
> NSTEP = 1 TIME(PS) = 140.002 TEMP(K) = 302.00 PRESS =
> -26.8
> Etot = -177479.4708 EKtot = 44538.7031 EPtot =
> -222018.1739
> BOND = 1426.7920 ANGLE = 3707.7449 DIHED =
> 5935.2323
> 1-4 NB = 1670.6042 1-4 EEL = 17671.6822 VDWAALS =
> 26333.7407
> EELEC = -278763.9704 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 19459.9489 VIRIAL = 19877.3290 VOLUME =
> 720868.8133
> Density =
> 1.0216
>
> ------------------------------------------------------------------------------
>
>
> NSTEP = 2 TIME(PS) = 140.004 TEMP(K) = 306.70 PRESS =
> -68.3
> Etot = -177516.1147 EKtot = 45231.9414 EPtot =
> -222748.0561
> BOND = 1315.2206 ANGLE = 3539.3545 DIHED =
> 5913.0637
> 1-4 NB = 1666.0066 1-4 EEL = 17666.0559 VDWAALS =
> 26288.0099
> EELEC = -279135.7674 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 19498.5145 VIRIAL = 20561.1439 VOLUME =
> 720867.0247
> Density =
> 1.0216
>
>
>
> Thanks,
> Xiaodong
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
    _______________________________________________
    AMBER mailing list
    AMBER.ambermd.org
    http://lists.ambermd.org/mailman/listinfo/amber
    This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator.

This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 05 2021 - 11:00:03 PST
Custom Search