AMBER Archive (2008)

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

From: N.R. Jena (nrjena_at_gmail.com)
Date: Thu Dec 04 2008 - 07:08:45 CST

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