AMBER Archive (2008)

Subject: Re: AMBER: steered MD

From: Germain Vallverdu (germain.vallverdu_at_lcp.u-psud.fr)
Date: Wed Sep 10 2008 - 07:10:49 CDT

Yes, thank you, I applied the newest bugfixes_all and I do not have this
problem. But If I write a dist.RST like that :

# change phi de r2=0 a r2a = 180 degre
&rst
  iat=21,22,24,25,
  r1 =-360., r2 = 0., r3 = 0. r4 =360.,
  r1a=-360., r2a=180., r3a=180. r4a=360.,
  rk2=5000., rk3=5000.,
/

sander does not read all the tags and keeps its default for r1 r4 ect
... This is the results in the mdout file :

 RESTRAINTS:
 Requested file redirections:
  DISANG = dist.RST
  DUMPAVE = phi_vs_t
  LISTIN = POUT
  LISTOUT = POUT
 Restraints will be read from file: dist.RST
Here are comments from the DISANG input file:
# change phi de r2=0 a r2a = 180
degre

******
 CA2 ( 21)-CB2 ( 22)-CG2 ( 24)-CD1 ( 25) NSTEP1= 0
NSTEP2= 50000
R1 =-100.000 R2 = 0.000 R3 = 0.000 R4 = 100.000 RK2 =5000.000 RK3 =
5000.000
R1A= 80.000 R2A= 180.000 R3A= 180.000 R4A= 280.000 RK2A=5000.000 RK3A=
5000.000
 Rcurr: -0.131 Rcurr-(R2+R3)/2: 0.131 MIN(Rcurr-R2,Rcurr-R3):
0.131
                       Number of restraints read = 1

                  Done reading weight changes/NMR restraints

Actually, it is not a problem because the default values will do what I
want but I would like to know if the syntax I used is the good one ?

Thanks a lot for your help.

Germain

Adrian Roitberg a écrit :
> Apply all patches to amber please.
> This is a problem solved by one of the bugfixes, related to the
> internal setting for R4A by default.
>
> Adrian
>
>
> Germain Vallverdu wrote:
>> This is the dist.RST file :
>>
>> # change phi de r2=0 a r2a = 180 degre
>> &rst iat=21,22,24,25, r2=0., rk2=5000., r2a=180., /
>>
>>
>> I tried with that :
>>
>> # change phi de r2=0 a r2a = 180 degre
>> &rst iat=21,22,24,25, r2=0., rk2=5000., r2a=180., r4a=360., /
>>
>>
>> But it does not work :
>>
>> Here is the input file (mdin) :
>>
>> steered MD sur phi
>> &cntrl
>> nstlim=50000, dt=0.001,
>> irest=0, ntx=1, iwrap=1, ig=100908
>> ntpr=1000, ntwr=1000, ntwx=100,
>> tempi=300.0, temp0=300.0, ntt=3, gamma_ln=1.0,
>> ntb=2, pres0=1.0, ntp=1, taup=2.0,
>> ntc=2, ntf=2,
>> cut=10.0,
>> jar=1,
>> /
>> &wt type='DUMPFREQ', istep1=1, /
>> &wt type='END', /
>> DISANG=steeredcoord
>> DUMPAVE=phi_vs_t
>> LISTIN=POUT
>> LISTOUT=POUT
>>
>> Thanks
>>
>> Germain
>>
>>
>>
>> Carlos Simmerling a écrit :
>>> can you show us the dist.RST file?
>>>
>>> On Wed, Sep 10, 2008 at 6:26 AM, Germain Vallverdu
>>> <germain.vallverdu_at_lcp.u-psud.fr> wrote:
>>>
>>>> Hello AMBER !
>>>>
>>>> I am trying to do a steered MD with the following dist.RST file :
>>>>
>>>> # change phi de r2=0 a r2a = 180 degre
>>>> &rst iat=21,22,24,25, r2=0., rk2=5000., r2a=180., /
>>>>
>>>> But the run stops at the beginning with this error message :
>>>>
>>>> ******
>>>> CA2 ( 21)-CB2 ( 22)-CG2 ( 24)-CD1 ( 25) NSTEP1= 0
>>>> NSTEP2=
>>>> 50000
>>>> R1 =-100.000 R2 = 0.000 R3 = 0.000 R4 = 100.000 RK2 =5000.000
>>>> RK3 =
>>>> 5000.000
>>>> R1A=-100.000 R2A= 180.000 R3A= 180.000 R4A= 100.000 RK2A= 0.000
>>>> RK3A=
>>>> 0.000
>>>> Rcurr: -0.131 Rcurr-(R2+R3)/2: 0.131 MIN(Rcurr-R2,Rcurr-R3):
>>>> 0.131
>>>> ERROR: r1 -> r4 (and r1a -> r4a) must be monotonically increasing;
>>>> Offending restraint:
>>>> ******
>>>> CA2 ( 21)-CB2 ( 22)-CG2 ( 24)-CD1 ( 25) NSTEP1= 0
>>>> NSTEP2=
>>>> 50000
>>>> R1 =-100.000 R2 = 0.000 R3 = 0.000 R4 = 100.000 RK2 =5000.000
>>>> RK3 =
>>>> 5000.000
>>>> R1A=-100.000 R2A= 180.000 R3A= 180.000 R4A= 100.000 RK2A= 0.000
>>>> RK3A=
>>>> 0.000
>>>>
>>>> I tried to defined r4a into the dist.RST file but it does not work.
>>>>
>>>> As you saw my coordinate is a dihedral angle and r4a is too small.
>>>>
>>>> Thanks
>>>>
>>>> Germain
>>>>
>>>>
>>>> --
>>>> Germain Vallverdu
>>>> Laboratoire de Chimie Physique
>>>> Université Paris Sud 11
>>>> germain.vallverdu_at_lcp.u-psud.fr
>>>> 01 69 15 30 38 / 06 88 59 08 87
>>>> Chacun de nous a son étoile. Suivons la en nous félicitant de la
>>>> voir chaque
>>>> jour un peu plus loin ! (V. Grignard)
>>>> -----------------------------------------------------------------------
>>>> The
>>>> AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To
>>>> unsubscribe,
>>>> send "unsubscribe amber" (in the *body* of the email) to
>>>> majordomo_at_scripps.edu
>>>>
>>>
>>>
>>>
>>>
>>
>> --
>> Germain Vallverdu
>> Laboratoire de Chimie Physique
>> Université Paris Sud 11
>> germain.vallverdu_at_lcp.u-psud.fr
>> 01 69 15 30 38 / 06 88 59 08 87
>> /Chacun de nous a son étoile. Suivons la en nous félicitant de la
>> voir chaque jour un peu plus loin !/ (V. Grignard)
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To
>> unsubscribe, send "unsubscribe amber" (in the *body* of the email) to
>> majordomo_at_scripps.edu
> 

-- 
Germain Vallverdu
Laboratoire de Chimie Physique
Université Paris Sud 11
germain.vallverdu_at_lcp.u-psud.fr
01 69 15 30 38 / 06 88 59 08 87
/Chacun de nous a son étoile. Suivons la en nous félicitant de la voir 
chaque jour un peu plus loin !/ (V. Grignard)
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu