I've had to do this myself a few times, even for relatively common atom types like halogens.
Editing the source code seems like overkill for a trivial issue like this, and could it maybe cause problems with patches, if mdread.f was affected? It also means you have to remember to redo this whenever you upgrade.
For future versions, would it be possible for these radii to be specifiable via an frcmod file (or similar), to avoid having to edit the source code?
Just a thought...
Paul
-----Original Message-----
From: Cuiyl [mailto:cuiyinglukitty.gmail.com]
Sent: 14 March 2013 08:58
To: AMBER Mailing List
Subject: Re: [AMBER] Bad atom type: fe in MMPBSA calculations
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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Mar 14 2013 - 03:30:02 PDT
