Re: [AMBER] Bad atom type: fe in MMPBSA calculations

From: siddharth kesharwani <siddharthnipermohali.gmail.com>
Date: Thu, 14 Mar 2013 14:48:30 +0530

Dear Cuiyl
There are 2 places where you are required to add the values, i am
 attaching the mdread.f file in the attachment and you go through the file
and identify the places where the changes have been named for the Fe and
then again re-install Amber

hope this helps you out
*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 2:27 PM, Cuiyl <cuiyinglukitty.gmail.com> wrote:

> 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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> >>
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>
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Received on Thu Mar 14 2013 - 02:30:05 PDT
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