Hi, Carlos,
Thanks for your help.
The input file resulted in error is 02_Heat.in, which was pasted from the tutorial web site:
"
Lipid 128 heating 100K
&cntrl
imin=0, ! Molecular dynamics
ntx=1, ! Positions read formatted with no initial velocities
irest=0, ! No restart
ntc=2, ! SHAKE on for bonds with hydrogen
ntf=2, ! No force evaluation for bonds with hydrogen
tol=0.0000001, ! SHAKE tolerance
nstlim=2500, ! Number of MD steps
ntt=3, ! Langevin thermostat
gamma_ln=1.0, ! Collision frequency for Langevin thermostat
ntr=1, ! Restrain atoms using a harmonic potential
! (See the GROUP input below)
ig=-1, ! Random seed for Langevin thermostat
ntpr=100,
ntwr=10000,
ntwx=100, ! Write to trajectory file every ntwx steps
dt=0.002, ! Timestep (ps)
nmropt=1, ! NMR restraints will be read (See TEMP0 control below)
ntb=1,
ntp=0,
cut=10.0,
ioutfm=1, ! Write a binary (netcdf) trajectory
ntxo=2, ! Write binary restart files
/
&wt
type='TEMP0', ! Varies the target temperature TEMP0
istep1=0, ! Initial step
istep2=2500, ! Final step
value1=0.0, ! Initial temp0 (K)
value2=100.0 / ! final temp0 (K)
&wt type='END' / ! End of varying conditions
Hold lipid fixed
10.0 ! Force constant (kcal/(mol Angstroms^2))
RES 1 384 ! Choose residues
END
END ! End GROUP input
"
However, there is something else that concerns me. I am using Amber 18;I have used AMBERHOME/dat/charmmlipid2amber/charmmlipid2amber.csv to convert the lipid PDB format; the box dimension estimated by vmd_box_dims.sh deviated from the value on tutorial web by about 15%; I could find the leaprc.ff12SB so I sourced the leaprc.ff14SB in xleap.
I hope these information is helpful.
Best regards,
Wang Wei
At 2021-07-08 21:18:42, "Carlos Simmerling" <carlos.simmerling.gmail.com> wrote:
>Please include the I put file too, it looks like an error reading your
>restraints but we can't see what you put in the input.
>
>On Thu, Jul 8, 2021, 9:00 AM 王维 <wangwei1619.yeah.net> wrote:
>
>> Hi, all,
>>
>>
>> I am following the tutorial Tutorial 1.7 An Amber Lipid Force Field
>> Tutorial: Lipid14. When I started to heat the system, I get a output as
>> "Stop PMEMD Terminated Aborally", and the last several rows of the
>> 02_Heat.out file is:
>> "
>> 5. REFERENCE ATOM COORDINATES
>>
>>
>> default_name
>>
>> ----- READING GROUP 1; TITLE:
>> Hold lipid fixed
>>
>>
>>
>> GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
>>
>>
>> rfree: Error decoding variable 4 2 from:
>> RES 1 384 !
>> "
>> I used the command "pmemd" but not the "pmemd.CUPD" since I am learning
>> Amber in a virtual machine.
>> Is there any way to fix this problem?
>> Thanks for help.
>>
>>
>> Best regards,
>> Wang Wei
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Fri Jul 09 2021 - 00:30:02 PDT
