[SOLVED] MOLCAS with TINKER: Calculation Won't Start

dommett110 · 2017-05-12 17:14:40

Hi all,

I am looking to run MOLCAS with the TINKER interface. I am using MOLCAS 8.0@UU binaries, and have downloaded the Tools directory from source, and TINKER 6.3.3. I have managed to compile Tinker with the QMMM interface using the get_tinker script, and both Tinker and MOLCAS can run independently without any issues.

The problem comes when I try to run the QMMM simulation using the espf module. To start with, I am following the Molcas/TINKER example as given in the manual, for Aspartic acid. My input files are:

asp.input:

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

&Seward

&Espf
        External = Tinker
        LAMorok

asp.xyz:

16 ASP
1 N3 -0.040452 0.189961 0.173219 448 2 6 14 15
2 CT -0.011045 -0.060807 1.622395 449 1 3 7 11
3 C 1.446535 -0.110535 2.028518 450 2 4 5
4 O 1.902105 0.960982 2.409042 452 3
5 O 2.137861 -0.898168 1.387158 452 3
6 H 0.559257 -0.496270 -0.262338 451 1
7 CT -0.789906 -1.336520 1.982558 216 2 8 12 13
8 C -2.256402 -1.184505 1.571038 218 7 9 10
9 O2 -2.460769 -0.949098 0.356151 219 8
10 O2 -3.120135 -1.188969 2.465678 219 8
11 H1 -0.478878 0.773493 2.145163 453 2
12 HC -0.356094 -2.194944 1.466324 217 7
13 HC -0.720511 -1.505463 3.058628 217 7
14 H -0.996208 0.061130 -0.151911 451 1
15 H 0.304306 1.116522 -0.018698 451 1
16 HLA -0.283317 -0.506767 1.748300 2999 2 7

asp.key:

parameters ./amber99.prm
QMMM 8
QM -8 10 7 12 13
MM 2
LA 16
* Add the atom type for the LA
atom 2999 99 HLA "Hydrogen Link Atom" 1 1.008 0
charge -2 0.0
charge -11 0.0
QMMM-MICROITERATION ON

These are taken from p174-175 of the manual for Molcas v8.0.

When I run

$molcas asp.input -f

, I get the following error message in the log file, where the $PATHTO replaces the working directory:

asp.log:

()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()


 TINKER keyword found, run $TINKER/tkr2qm_s asp.xyz>asp.Tinker.log
 ###############################################################################
 ###############################################################################
 ###                                                                         ###
 ###                                                                         ###
 ###    File $PATHTO/asp-test/Molcas-10
 ###    is not found                                                         ###
 ###                                                                         ###
 ###                                                                         ###
 ###############################################################################
 ###############################################################################
--- Stop Module:  gateway at Fri May 12 16:44:06 2017 /rc= _INPUT_ERROR_ ---

    User input error

    ...................................................................................................
    ...................................................................................................
    .....Sorry to interrupt the festivities, Dave, but I think we've got a problem.....................
    .....It can only be attributable to human error....................................................
    ...................................................................................................

Non-zero return code - check program input/output
--- Stop Module:  auto at Fri May 12 16:44:06 2017 /rc= _INPUT_ERROR_ ---

Does any one have any suggestions as to what this error is? I have found no reference for this Molcas-10 file and so am a bit stuck at this point!

As a second point, if I can overcome this problem, I eventually aim to do CASSCF QM/MM and optimize conical intersections. Is this possible? I can optimize the conical intersection with CASSCF in vacuum, but am looking to now incorporate a frozen MM environment too.

Thank you for taking the time to read and help with my problem

Best wishes

Michael Dommett

Ignacio · 2017-05-13 09:10:47

dommett110 wrote:

 TINKER keyword found, run $TINKER/tkr2qm_s asp.xyz>asp.Tinker.log
Does any one have any suggestions as to what this error is? I have found no reference for this Molcas-10 file and so am a bit stuck at this point!

Have you defined the TINKER environment variable? Does $TINKER/tkr2qm_s.asp exist? Do you have any message in the asp.err file?

Add these lines at the top of asp.input:

> COPY $CurrDir/$Project.xyz $WorkDir/$Project.xyz
> COPY $CurrDir/$Project.key $WorkDir/$Project.key

dommett110 wrote:

parameters ./amber99.prm

Is this correct? Do you have the amber99.prm file in the scratch directory (that is where whe tkr2qm_s job is run from)? Better specify the absolute path to the amber99.prm file.

As a second point, if I can overcome this problem, I eventually aim to do CASSCF QM/MM and optimize conical intersections. Is this possible? I can optimize the conical intersection with CASSCF in vacuum, but am looking to now incorporate a frozen MM environment too.

It should kind of work with 8.0, but it will work better with later versions, where we have actual non-adiabatic coupling vectors.

dommett110 · 2017-05-13 11:27:55

Hi Ignacio, Thanks for your help and taking the time to reply.

Have you defined the TINKER environment variable? Does $TINKER/tkr2qm_s.asp exist?
Add these lines at the top of asp.input ...

I have defined the $TINKER variable in my path, but I will xplicitly give the $TINKER variable in the asp.input file. This hasnt helped matters though. The same goes with the addition of the COPY $CurrDir/$Project.xyz $WorkDir/$Project.xyz ... commands.

I have also given the absolute path to the amber99 parameter file, but also this hasnt helped.

Do you have any message in the asp.err file?

I should have added thsi in the original post, sorry for that. Having made the changes you suggest above, the message in asp.err reads:

--- Start Module: auto at Sat May 13 11:06:29 2017
--- Start Module: gateway at Sat May 13 11:06:29 2017
At line 44 of file getxyz.f (unit = 5, file = 'stdin')
Fortran runtime error: End of file
--- Stop Module:  gateway at Sat May 13 11:06:29 2017 /rc= _INPUT_ERROR_ ---
*** files:   xmldump
    saved to directory $PATHTO/asp-test

--- Stop Module:  auto at Sat May 13 11:06:29 2017 /rc= _INPUT_ERROR_ ---

Have you any further suggestions? Thank you for your help

Michael

Ignacio · 2017-05-13 13:05:12

That file (getxyz.f) is part of Tinker, so it's Tinker that's failing. Inspecting the code at line 44, it seems it didn't find the asp.xyz file and it's trying to get a filename from an interactive prompt, but maybe you are running this inside a script or without a proper stdin. I can finally reproduce your error if I:

1. Do not copy the asp.xyz to the $WorkDir
2. Run "nohup molcas asp.input -f"

without "nohup" it just hangs (waiting for the user to input a filename), and if I copy the asp.xyz file it runs successfully.

So all I can say is that apparently you are not copying the asp.xyz file to the scratch directory correctly. Can you check if the file is actually there?

dommett110 · 2017-05-14 15:15:14

Thanks Ignacio! You have found the source of the problem -

So all I can say is that apparently you are not copying the asp.xyz file to the scratch directory correctly. Can you check if the file is actually there?

Indeed I (stupidly) had not added the '>' to the front of the COPY commands at the top of the asp.input file.

It is working now and I am able to run further tests. Thanks so much for your help smile

Michael

Molcas Forum

Announcement

#1 2017-05-12 17:14:40

[SOLVED] MOLCAS with TINKER: Calculation Won't Start

#2 2017-05-13 09:10:47

Re: [SOLVED] MOLCAS with TINKER: Calculation Won't Start

#3 2017-05-13 11:27:55

Re: [SOLVED] MOLCAS with TINKER: Calculation Won't Start

#4 2017-05-13 13:05:12

Re: [SOLVED] MOLCAS with TINKER: Calculation Won't Start

#5 2017-05-14 15:15:14

Re: [SOLVED] MOLCAS with TINKER: Calculation Won't Start

Board footer