Dear Siddharth kesharwani:
Thank you for your kindly help. I added the parameters of FE in
mdread.f file as follows:
if ( gbsa == 1 ) then
……
……
else if (atype(1:1) == 'FE' .or. atype(1:1) == 'Fe') then
x(l165-1+i) = 0.78d0 + 1.4d0
x(l170-1+i) = 0.00000d0
x(l175-1+i) = -0.00000d0
x(l180-1+i) = -0.00000d0
x(l185-1+i) = 0.00000d0
……
……
end if
end do ! i=1,natom
!
else if ( gbsa == 2 ) then
……
……
else if (atype(1:1) == 'FE' .or. atype(1:1) == 'Fe') then
x(l165-1+i) = 0.78d0 + 1.4d0
……
……
Can you suggest me whether it is correct?
2013/3/14 siddharth kesharwani <siddharthnipermohali.gmail.com>:
> Dear Cuiyl
> Even i was facing the similar problem and this why the error has occured,
> This error has occured because there is no Atomic radii of Fe in the
> mdread.f file and you need to add the radius of Fe in that and you will
> require to re-install Amber again after adding the atomic radius of Fe.
> *Thanks & Regards*
> *
> *
> *Siddharth S . kesharwani
> M.S.(Pharm.) Scholar
> Department of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research (NIPER)
> Sector 67, S.A.S. Nagar, (Punjab) INDIA-160062
> Mob. 09646948577*
>
>
> On Thu, Mar 14, 2013 at 10:33 AM, Cuiyl <cuiyinglukitty.gmail.com> wrote:
>
>> Dear all amber users:
>>
>> I've been simulating a protein system containing Fe atoms. The
>> Fe atoms are bound to residues in the protein. I am trying to do an
>> MMPBSA calculation on my protein complex. Previous MMPBSA caIculations
>> of PB/GB and entropy ended normally. But when I try to do an energy
>> decomposition I get an the error:
>>
>> "bad atom type: fe
>> bad atom type: fe
>> bad atom type: fe
>> bad atom type: fe
>> bad atom type: fe
>> bad atom type: fe
>> bad atom type: fe
>> close failed in file object destructor:
>> IOError: [Errno 9] Bad file descriptor
>> close failed in file object destructor:
>> IOError: [Errno 9] Bad file descriptor
>> close failed in file object destructor:
>> IOError: [Errno 9] Bad file descriptor
>> close failed in file object destructor:
>> IOError: [Errno 9] Bad file descriptor
>> close failed in file object destructor:
>> IOError: [Errno 9] Bad file descriptor
>> close failed in file object destructor:
>> IOError: [Errno 9] Bad file descriptor
>> close failed in file object destructor:
>> IOError: [Errno 9] Bad file descriptor"
>>
>> I've check the mm_pbsa_calceneent.pm file, it includes a parameter line
>> for FE.
>> "FE" => 1.300 + 1.400,
>> Any ideas of how to overcome this problem?
>>
>> Thanks,
>> Cuiyl
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Mar 14 2013 - 02:30:03 PDT
