Dear Siddharth kesharwani:
Thank you for your kindly help. It works well now!
2013/3/14 siddharth kesharwani <siddharthnipermohali.gmail.com>:
> 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
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 18 2013 - 02:00:02 PDT
