I checked the min1.out file, following are the error massage:
QM ATOM VALIDATION: nquant has a value of 0
which is bigger than natom of 73626. Need 0 < nquant <= natom.
SANDER BOMB in subroutine validate_qm_atoms
nquant illegal
Need 0 < nquant <= natom
I rewrite the min.in:
&qmmm
iqmatoms='.6068-6075,6098-6105,8252-8261,11263-11268,13185-13187,13190-13191,13195-13197,13201-13202,13204-13225,13237-13242',
qmcharge=-1,
qm_theory=PM3,
qmshake=1,
qm_ewald=1, qm_pme=1
/
but the error also occurred. How to set the value of iqmatoms?
2013/9/27 Cuiyl <cuiyinglukitty.gmail.com>
> Dear Amber users:
>
> I am trying to use QM/MM in AMBER11, it stopped in the minimization
> step. My min.in file are as following:
> initial minimization for QM/MM
> &cntrl
> imin=1,
> maxcyc=5000,
> ncyc=2500,
> ntb=1,
> cut=8.0,
> ntc=2,
> ntf=2,
> ifqnt=1
> /
> &qmmm
>
> iqmatoms='.6068-6075,6098-6105,8252-8261,11263-11268,13185-13187,13190-13191,13195-13197,13201-13202,13204-13225,13237-13242',
> qmcharge=-1,
> qmtheory=1,
> qmshake=1,
> qm_ewald=1, qm_pme=1
> /
>
> And I got the following error messages:
>
> librdmacm: assuming: 4
> libibverbs: Fatal: couldn't read uverbs ABI version.
> [[3377,1],4]: A high-performance Open MPI point-to-point messaging module
> was unable to find any relevant network interfaces:
>
> Module: OpenFabrics (openib)
> Host: cu18
>
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 0 with PID 19628 on
> node cu18 exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
>
> How can I solve the problem? Thank you!
> --
>
> *Ying-Lu Cui*
> State Key Laboratory of Theoretical and Computational Chemistry,
> Institute of Theoretical Chemistry,
> Jilin University,
> Changchun 130023,
> P. R. China
>
>
--
*崔颖璐*
中国 吉林省 长春市
吉林大学理论化学研究所
理论化学计算国家重点实验室
*Ying-Lu Cui*
State Key Laboratory of Theoretical and Computational Chemistry,
Institute of Theoretical Chemistry,
Jilin University,
Changchun 130023,
P. R. China
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Received on Thu Sep 26 2013 - 20:30:02 PDT
