AMBER Archive (2008)

Subject: Re: AMBER: MM/GBSA Error during deccomposition

From: N.R. Jena (nrjena_at_gmail.com)
Date: Thu Dec 04 2008 - 22:13:44 CST

Hi Florent Barbault, Cristina and other Amber-users,

Now I got rid of this decomposition error. Actually this had happened
to me due to bad defination of terms under heading of @DECOMP.

Thanks to everybody.

 Thu, Dec 4, 2008 at 9:08 PM, N.R. Jena <nrjena_at_gmail.com> wrote:
> Hi Cristina,
>
> Thanks a lot. My snapshot_lig.all.out file looks like as follows.
> There is no such ***** mark. Here I got total, back bone and side
> chain energies, though I do not know what these 4 columns of energies
> signify ? Do you know? If I will look into my snapshot_rec.all.out and
> snapshot_com.all.out files, there are exactly 343 and 344 TDC, SDC and
> BDC energies (these are same as the number of residues). As my ligand
> contains 47 atoms, the TDC, BDC and SDC values should be 47, why there
> are 50 energies (I had extracted 50 snapshots of each)? Actually the
> error indicating residue 345 belongs to a water molecule. If I am
> right, the snapshots I created earlier does not contain any water
> (total number of atoms is exactly same as the complex has, without
> water) I am also attaching the script I used to extract snapshots. If
> any body has any idea, please share with me.
>
> MM
> GB
> MS
> 1
> TDC 1 67.180 13.360 -121.839 -28.144 0.000
> SDC 1 67.180 13.360 -121.839 -28.144 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 2
> TDC 1 69.920 17.018 -124.297 -27.717 0.000
> SDC 1 69.920 17.018 -124.297 -27.717 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 3
> TDC 1 63.089 20.509 -124.450 -26.445 0.000
> SDC 1 63.089 20.509 -124.450 -26.445 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 4
> TDC 1 68.216 14.202 -128.690 -25.484 0.000
> SDC 1 68.216 14.202 -128.690 -25.484 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 5
> TDC 1 62.793 18.799 -123.606 -24.894 0.000
> SDC 1 62.793 18.799 -123.606 -24.894 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 6
> TDC 1 62.700 14.848 -121.555 -26.533 0.000
> SDC 1 62.700 14.848 -121.555 -26.533 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 7
> TDC 1 64.190 17.568 -126.150 -24.702 0.000
> SDC 1 64.190 17.568 -126.150 -24.702 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 8
> TDC 1 71.073 11.825 -123.056 -28.317 0.000
> SDC 1 71.073 11.825 -123.056 -28.317 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 9
> TDC 1 60.365 15.591 -119.511 -27.499 0.000
> SDC 1 60.365 15.591 -119.511 -27.499 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 10
> TDC 1 71.392 14.650 -121.009 -29.246 0.000
> SDC 1 71.392 14.650 -121.009 -29.246 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 11
> TDC 1 65.853 15.336 -124.187 -25.066 0.000
> SDC 1 65.853 15.336 -124.187 -25.066 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 12
> TDC 1 70.117 14.209 -125.118 -27.473 0.000
> SDC 1 70.117 14.209 -125.118 -27.473 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 13
> TDC 1 69.602 14.946 -124.814 -27.357 0.000
> SDC 1 69.602 14.946 -124.814 -27.357 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 14
> TDC 1 66.394 16.566 -127.065 -25.937 0.000
> SDC 1 66.394 16.566 -127.065 -25.937 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 15
> TDC 1 70.530 13.048 -121.845 -28.838 0.000
> SDC 1 70.530 13.048 -121.845 -28.838 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 16
> TDC 1 67.443 13.417 -124.885 -27.260 0.000
> SDC 1 67.443 13.417 -124.885 -27.260 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 17
> TDC 1 72.679 13.940 -125.530 -27.166 0.000
> SDC 1 72.679 13.940 -125.530 -27.166 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 18
> TDC 1 69.294 15.625 -123.564 -26.095 0.000
> SDC 1 69.294 15.625 -123.564 -26.095 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 19
> TDC 1 70.930 14.125 -123.652 -28.720 0.000
> SDC 1 70.930 14.125 -123.652 -28.720 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 20
> TDC 1 79.824 22.574 -122.017 -28.655 0.000
> SDC 1 79.824 22.574 -122.017 -28.655 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 21
> TDC 1 66.611 16.380 -122.368 -27.708 0.000
> SDC 1 66.611 16.380 -122.368 -27.708 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 22
> TDC 1 69.946 13.943 -125.681 -27.301 0.000
> SDC 1 69.946 13.943 -125.681 -27.301 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 23
> TDC 1 60.982 16.255 -122.992 -27.858 0.000
> SDC 1 60.982 16.255 -122.992 -27.858 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 24
> TDC 1 63.148 18.873 -127.193 -25.703 0.000
> SDC 1 63.148 18.873 -127.193 -25.703 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 25
> TDC 1 83.744 15.711 -125.022 -29.266 0.000
> SDC 1 83.744 15.711 -125.022 -29.266 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 26
> TDC 1 66.692 15.964 -126.176 -26.025 0.000
> SDC 1 66.692 15.964 -126.176 -26.025 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 27
> TDC 1 67.322 18.473 -129.997 -24.808 0.000
> SDC 1 67.322 18.473 -129.997 -24.808 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 28
> TDC 1 68.079 12.301 -124.388 -25.584 0.000
> SDC 1 68.079 12.301 -124.388 -25.584 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 29
> TDC 1 67.538 13.807 -121.427 -26.685 0.000
> SDC 1 67.538 13.807 -121.427 -26.685 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 30
> TDC 1 69.782 15.502 -126.430 -24.691 0.000
> SDC 1 69.782 15.502 -126.430 -24.691 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 31
> TDC 1 58.395 16.441 -122.068 -26.057 0.000
> SDC 1 58.395 16.441 -122.068 -26.057 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 32
> TDC 1 80.858 17.766 -126.105 -26.337 0.000
> SDC 1 80.858 17.766 -126.105 -26.337 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 33
> TDC 1 62.593 16.650 -125.954 -25.872 0.000
> SDC 1 62.593 16.650 -125.954 -25.872 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 34
> TDC 1 71.204 15.576 -125.754 -26.605 0.000
> SDC 1 71.204 15.576 -125.754 -26.605 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 35
> TDC 1 61.674 17.291 -123.556 -25.262 0.000
> SDC 1 61.674 17.291 -123.556 -25.262 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 36
> TDC 1 64.856 18.513 -124.957 -26.198 0.000
> SDC 1 64.856 18.513 -124.957 -26.198 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 37
> TDC 1 70.137 14.507 -123.318 -27.363 0.000
> SDC 1 70.137 14.507 -123.318 -27.363 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 38
> TDC 1 63.718 14.552 -123.541 -27.217 0.000
> SDC 1 63.718 14.552 -123.541 -27.217 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 39
> TDC 1 62.511 14.864 -122.537 -26.124 0.000
> SDC 1 62.511 14.864 -122.537 -26.124 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 40
> TDC 1 62.273 16.962 -121.710 -25.408 0.000
> SDC 1 62.273 16.962 -121.710 -25.408 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 41
> TDC 1 69.897 15.319 -121.456 -29.464 0.000
> SDC 1 69.897 15.319 -121.456 -29.464 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 42
> TDC 1 77.775 13.343 -121.976 -28.736 0.000
> SDC 1 77.775 13.343 -121.976 -28.736 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 43
> TDC 1 65.133 15.304 -122.939 -25.916 0.000
> SDC 1 65.133 15.304 -122.939 -25.916 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 44
> TDC 1 59.239 15.773 -123.393 -27.014 0.000
> SDC 1 59.239 15.773 -123.393 -27.014 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 45
> TDC 1 76.535 17.063 -125.641 -24.579 0.000
> SDC 1 76.535 17.063 -125.641 -24.579 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 46
> TDC 1 66.396 16.062 -129.434 -25.699 0.000
> SDC 1 66.396 16.062 -129.434 -25.699 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 47
> TDC 1 71.360 15.335 -122.560 -25.340 0.000
> SDC 1 71.360 15.335 -122.560 -25.340 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 48
> TDC 1 71.015 15.646 -124.756 -27.562 0.000
> SDC 1 71.015 15.646 -124.756 -27.562 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 49
> TDC 1 66.569 15.271 -124.391 -27.403 0.000
> SDC 1 66.569 15.271 -124.391 -27.403 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
> 50
> TDC 1 58.586 16.336 -122.177 -25.737 0.000
> SDC 1 58.586 16.336 -122.177 -25.737 0.000
> BDC 1 0.000 0.000 0.000 0.000 0.000
>
> script for snapshot extraction:
>
> @GENERAL
> PREFIX snapshot
> PATH ./snapshot
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./complex4_min.top
> RECPT ./1q3d_H.top
> LIGPT ./H894_H.top
> GC 1
> AS 0
> DC 0
> MM 0
> GB 0
> PB 0
> MS 0
> NM 0
> @MAKECRD
> BOX YES
> NTOTAL 57739
> NSTART 1
> NSTOP 600
> NFREQ 12
> NUMBER_LIG_GROUPS 1
> LSTART 5475
> LSTOP 5521
> NUMBER_REC_GROUPS 1
> RSTART 1
> RSTOP 5474
> @TRAJECTORY
> TRAJECTORY ./traj_complex4_min_SOLV10.crd
> TRAJECTORY ./traj_complex4_min_SOLV11.crd
> TRAJECTORY ./traj_complex4_min_SOLV12.crd
>
>
>
> On Thu, Dec 4, 2008 at 7:27 PM, Cristina Sisu <csds2_at_cam.ac.uk> wrote:
>> Hi Jena,
>>
>> If you check the /snaphot_lig_all.out / you'll see that
>> in the first snapshot, (see 1) in the residue 435 (residue number in
>> column 2) ,the corresponding value in column 3 (the one for
>> electrostatic contribution - BELE I believe ) might be something like
>> this: ********** , in other words not a number. Why does something like
>> this happens I am not sure. To bypass this problem I used to remove that
>> snapshot from the list of snapshots or just remove the residue from
>> comparison.
>>
>> Hope that helps,
>> Cristina
>>
>> N.R. Jena wrote:
>>> Thanks Florent Barbault. It seems to me that my definations of LIGRES,
>>> LIGPRI and LIGMAP are okay. I need to know what is the meaning of this
>>> error. This might help me to track its cause.
>>>
>>> On Thu, Dec 4, 2008 at 4:32 AM, Barbault Florent
>>> <florent.barbault_at_paris7.jussieu.fr> wrote:
>>>
>>>> Hello
>>>>
>>>> I already had this. For myself, this problem has arose from a bad definition
>>>> of LIGRES, LIGPRI and LIGMAP. However, I still didn't understand what was
>>>> the meaning of "missing BELE...". So my suggestion is to have a look on the
>>>> ligand definition... Hope this will help you.
>>>>
>>>> Regards
>>>> Florent Barbault
>>>>
>>>>
>>>> On Wed, 3 Dec 2008 20:01:04 +0800
>>>> "N.R. Jena" <nrjena_at_gmail.com> wrote:
>>>>
>>>>> Dear Amber users,
>>>>>
>>>>> I got an error like "Missing BELE for MM in 1 (residue 435)" while
>>>>> decomposition of complex. Residue 435
>>>>> corresponds to one of the water molecules of the water box. I followed
>>>>> the previous question-answer section in this regard, but could not
>>>>> find any answer. my input file is like this:
>>>>>
>>>>> @GENERAL
>>>>> PREFIX snapshot
>>>>> PATH ./snapshot/
>>>>> COMPLEX 1
>>>>> RECEPTOR 1
>>>>> LIGAND 1
>>>>> COMPT ./complex4_min_Ions.top
>>>>> RECPT ./1q3d_H.top
>>>>> LIGPT ./H894_H.top
>>>>> GC 0
>>>>> AS 0
>>>>> DC 1
>>>>> MM 1
>>>>> GB 1
>>>>> PB 0
>>>>> MS 0
>>>>> NM 0
>>>>> @PB
>>>>> PROC 2
>>>>> REFE 0
>>>>> INDI 1.0
>>>>> EXDI 80
>>>>> SCALE 2
>>>>> LINIT 1000
>>>>> PRBRAD 1.4
>>>>> ISTRNG 0
>>>>> RADIOPT 0
>>>>> NPOPT 1
>>>>> CAVITY_SURFTEN 0.0072
>>>>> CAVITY_OFFSET 0.00
>>>>> SURFTEN 0.0072
>>>>> SURFOFF 0.00
>>>>> CUTRES 12
>>>>> FILLRATIO 2
>>>>> @MM
>>>>> DIELC 1.0
>>>>> @GB
>>>>> IGB 1
>>>>> GBSA 2
>>>>> SALTCON 0.00
>>>>> EXTDIEL 80
>>>>> INTDIEL 1.0
>>>>> SURFTEN 0.0072
>>>>> SURFOFF 0.00
>>>>> @MS
>>>>> PROBE 0.0
>>>>> @DECOMP
>>>>> DCTYPE 2
>>>>> COMREC 1-5474
>>>>> COMLIG 5475-5521
>>>>> COMPRI 1-5521
>>>>> RECRES 1-5474
>>>>> RECPRI 1-5474
>>>>> RECMAP 1-5474
>>>>> LIGRES 1-47
>>>>> LIGPRI 1-47
>>>>> LIGMAP 5475-5521
>>>>>
>>>>> It will be quite helpful, if someone will guide me.
>>>>>
>>>>> With warm regards,
>>>>>
>>>>> (N.R. Jena)
>>
>> -----------------------------------------------------------------------
>> 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
>>
>
-----------------------------------------------------------------------
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