I am simulating a protein
I am having following error in minimization for which already tried changing
ntb values but didnt work.
At line 236 of file _getcor.f (unit = 9, file = 'min400.rst')
Fortran runtime error: End of file
while _getcor.f file line 236 is bold one
if(ntx == 1) then
do i = 1,nr3
v(i) = 0.d0
end do
if (writeflag) then
write(6,9008) title1
write(6,9009) tt
end if
line 236 close(lun, iostat=ier)
Kindly guide me if somebody has encountered this kind of error
On Tue, Feb 16, 2010 at 7:55 AM, sikander azam <syedazam2008.gmail.com>wrote:
> Hi Users,
>
> I am having a protein with Ca and Phosphate. I came to know through search
> that atom type for Calcium should be C0. In my pdb file it happens to be as
> under:
>
> HETATM 2809 C0 Ca2 A1356 4.902 31.422 21.076
> HETATM 2810 C0 Ca2 A1357 9.862 26.279 23.131
> HETATM 2811 P PO4 A1358 12.263 24.882 25.290
> HETATM 2812 O1 PO4 A1358 10.821 25.112 24.781
> HETATM 2813 O2 PO4 A1358 12.995 23.970 24.323
> HETATM 2814 O3 PO4 A1358 12.237 24.170 26.585
> HETATM 2815 O4 PO4 A1358 13.018 26.210 25.500
> TER 2816 P04 A1358
> END
>
>
> While I am having following output loading in xleap
>
> Loading PDB file: ./PON-15.pdb
> Unknown residue: Ca2 number: 355 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: Ca2 number: 356 type: Nonterminal
> Unknown residue: PO4 number: 357 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: Ca2 sequence: 356
> Created a new atom named: C0 within residue: .R<Ca2 356>
> Creating new UNIT for residue: Ca2 sequence: 357
> Created a new atom named: C0 within residue: .R<Ca2 357>
> Creating new UNIT for residue: PO4 sequence: 358
> Created a new atom named: P within residue: .R<PO4 358>
> Created a new atom named: O1 within residue: .R<PO4 358>
> Created a new atom named: O2 within residue: .R<PO4 358>
> Created a new atom named: O3 within residue: .R<PO4 358>
> Created a new atom named: O4 within residue: .R<PO4 358>
> total atoms in file: 2814
> Leap added 2769 missing atoms according to residue templates:
> 2769 H / lone pairs
> The file contained 7 atoms not in residue templates
>
>
> Kindly suggest me to remove these errors as I am using AMBER 10 with ff03.
>
>
> Best
>
>
>
> On Thu, Feb 4, 2010 at 3:48 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> > While In the following directory
>> >
>> > /usr/local/amber11/exe
>> >
>> > I found xleap but it is not running and giving error
>>
>> This means you have xleap from AMBERTools 1.3 built. AMBERTools 1.3
>> extracts
>> into the directory AMBER 11.
>>
>> > Error: you must set the AMBERHOME environment variable!
>>
>> This is the error. You need to set this environment variable. It is only
>> used by AMBERTools, not sander, pmemd etc so you would simply point this
>> at
>> AMBER11. e.g.
>>
>> for bash shell:
>> export AMBERHOME=/usr/local/amber11/
>>
>> for csh shell:
>> setenv AMBERHOME=/usr/local/amber11/
>>
>> Then xleap should run fine with AMBERHOME/exe/xleap (or by adding
>> $AMBERHOME/exe/) to your path.
>>
>> You should probably add the AMBERHOME definition to your .bashrc or .cshrc
>> file so it gets set everytime you login.
>>
>> Good luck,
>> Ross
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Mar 05 2010 - 00:30:03 PST
