Molcas Forum

Supervitux

Member

Registered: 2017-11-08

Posts: 2

MOLCAS with TINKER calculation won't start (File Molcas-10 not found)

Dear all,

I am trying to do a QM/MM calculation with Molcas with the Tinker-Interface for adenosine. I want to include the adenine in the QM-region and the sugar in the MM-region.

I am using a very reduced input, directly taken from the Molcas-Manual example file and created the xyz-File with Tinker's tool pdbxyz out of a pdb-file, yet I keep on getting the same error, seemingly the calculation does not even start.
Anyways I did tons of various calculations with the Manual-Example trying to find the source of my error, the manual-example ran without any problems with the exact same paths. Only after changing bonds or labeling in the .xyz file, it would give me the same error.

My input files are:

adenosin.inp:

> EXPORT  TINKER=$MOLCAS/tinker/bin
> COPY /home.aletheia/vbe/Bachelor/Rechnungen/QMMM/Vorrechnungen/adenosin.xyz $WorkDir/adenosin.xyz
> COPY /home.aletheia/vbe/Bachelor/Rechnungen/QMMM/Vorrechnungen/adenosin.key $WorkDir/adenosin.key

&Gateway
 Tinker
 Basis  =  STO-3G
 Group  =  Nosym

 &Seward

 &Espf
  External  =  Tinker
  LAMorok
End of Input

The adenosin.xyz File was created by the Tinker programme pdbxyz:

32  TEST 
 1 OH     29.480000   19.030000   21.760000  1244     2     9
 2 CT     30.620000   19.220000   20.900000  1118     1     3    10    11
 3 CT     31.330000   20.550000   21.070000  1121     2     4     6    12
 4 OS     30.490000   21.580000   20.640000  1123     3     5
 5 CT     30.040000   22.380000   21.700000  1124     4     7    16    18
 6 CT     31.750000   20.910000   22.570000  1126     3     7     8    13
 7 CT      30.490000   21.700000   22.990000  1128     5     6    14    15
 8 OH     32.910000   21.710000   22.480000  1249     6    17
 9 HO     29.074281   18.133259   21.583230  1245     1
10 H1     30.315365   19.100458   19.860285  1119     2
11 H1      31.329695   18.406702   21.051590  1120     2
12 H1      32.270000   20.410000   20.460000  1122     3
13 H1      31.950000   20.020000   23.210000  1127     6
14 HC     29.719092   21.005115   23.323069  1129     7
15 HC     30.763548   22.457603   23.724377  1130     7
16 H2      30.480000   23.390000   21.550000  1125     5
17 HO     33.213448   21.962526   23.398776  1250     8
18 N*      28.550000   22.490000   21.470000  1132     5    19    27
19 CK     27.590000   21.540000   21.670000  1136    18    20    28
20 NB     26.410000   21.950000   21.250000  1135    19    21
21 CB     26.620000   23.290000   20.850000  1134    20    22    27
22 CA     25.790000   24.290000   20.320000  1140    21    23    24
23 N2     24.490000   24.280000   20.200000  1142    22    29    30
24 NC     26.320000   25.450000   19.980000  1139    22    25
25 CQ     27.630000   25.560000   20.000000  1138    24    26    31
26 NC     28.540000   24.710000   20.400000  1137    25    27
27 CB     27.940000   23.560000   20.910000  1133    18    21    26
28 H5     27.810000   20.620000   22.120000  1145    19
29 H       24.050000   25.140000   19.830000  1143    23
30 H       23.980000   23.500000   20.520000  1144    23
31 H5     27.870000   26.460000   19.530000  1141    25
32 HLA   29.532027   22.417501   21.621588  2999     5    18     

adenosin.key:

* Change $PATH_TO_TINKER
parameters /opt/adm/molcas/molcas82-ubuntu-par/tinker/params/amber99.prm
QMMM 15
QM -19 31  
MM 18 
LA 32
* Add the atom type for the LA
atom   2999    99    HLA     "Hydrogen Link Atom"        1      1.008     0
QMMM-MICROITERATION ON

With this input I get an Input Error:

TINKER keyword found, run /opt/adm/molcas/molcas82-ubuntu-par/tinker/bin/tkr2qm_s adenosin.xyz>adenosin.Tinker.log
 ###############################################################################
 ###############################################################################
 ###                                                                         ###
 ###                                                                         ###
 ###    File Molcas-10 is not found                                          ###
 ###                                                                         ###
 ###                                                                         ###
 ###############################################################################
 ###############################################################################
--- Stop Module:  gateway at Wed Nov  8 15:25:42 2017 /rc= _INPUT_ERROR_ ---
Non-zero return code - check program input/output

respectively the Errorfile prints:

--- Start Module: gateway at Wed Nov  8 15:25:41 2017 
[ process      0]: xquit (rc =    112): _INPUT_ERROR_
--- Stop Module:  gateway at Wed Nov  8 15:25:42 2017 /rc= _INPUT_ERROR_ ---
*** files:   xmldump
    saved to directory /home.aletheia/vbe/Bachelor/Rechnungen/QMMM/Vorrechnungen

--- Stop Module:  auto at Wed Nov  8 15:25:42 2017 /rc= _INPUT_ERROR_ ---

Can anyone see what the reason for the Error is? Since there is no "File Molcas-10" involved, I am quite clueless at this point.
I would be very happy about any hint. I hope I provided all the necessary information.

Thank you in advance for taking time and dealing with my problem.

Best wishes

Vitus Besel

Last edited by Supervitux (2017-11-08 16:01:20)

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,011

Re: MOLCAS with TINKER calculation won't start (File Molcas-10 not found)

What does the file adenosin.Tinker.log say?

Supervitux

Member

Registered: 2017-11-08

Posts: 2

Re: MOLCAS with TINKER calculation won't start (File Molcas-10 not found)

It said that my frontier Bond is not defined correctly. So I realized that the MM does not request the last atom of the QM region, but rather the first atom of the MM region.
Thank you very much for taking the time to read my post and giving me the decisive hint for finding the problem.

Best wishes

Vitus Besel

niko

Member

From: Marseille

Registered: 2015-11-08

Posts: 59

Website

Re: MOLCAS with TINKER calculation won't start (File Molcas-10 not found)

I may add a general hint. After having built your xyz and key files, run Tinker utility analyze. It will fail if something is wrong with your files.