How did you load your protein force field? Did you use one of the
standard leaprc's down in $AMBERHOME/dat/leap/cmd?
My best guess is that you didn't load library files for N- and
C-terminal amino acids. For example, to load the params for ff94, you
need all three of: all_amino94.lib, all_aminoct94.lib &
all_aminont94.lib. The "ct" and "nt" versions contain the terminal
groups.
The leaprc's that ship with Amber generally load all these. So, if
you're making a custom one, you might try looking in, say,
leaprc.ff99SB, to see what all is frequently needed.
On Fri, Aug 12, 2011 at 10:11 PM, Yun Shi <yunshi09.gmail.com> wrote:
> Thanks Lachele!
>
> I initially thought TER card would take up one atom numbering, but it turned
> out not, meaning I do not have to renumbering subsequent atoms every time I
> add a TER card.
>
> So my oligosaccharide seems to be recognized by GLYCAM_06 ff.
>
> But when I loaded the protein-sugar complex into tleap with GLYCAM_06 ff, it
> seems those terminal amino acids were not recognized. I got screen info such
> as:
>
> Unknown residue: ASP number: 0 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> ...
> Unknown residue: PRO number: 434 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> ...
>
> But every amino acid residue (including terminal ones) had its new residue
> created, like
>
> ...
> Creating new UNIT for residue: PRO sequence: 435
> Created a new atom named: N within residue: .R<PRO 435>
> Created a new atom named: CA within residue: .R<PRO 435>
> Created a new atom named: C within residue: .R<PRO 435>
> Created a new atom named: O within residue: .R<PRO 435>
> Created a new atom named: CB within residue: .R<PRO 435>
> Created a new atom named: CG within residue: .R<PRO 435>
> Created a new atom named: CD within residue: .R<PRO 435>
> Created a new atom named: OXT within residue: .R<PRO 435>
> ...
>
> So why there is no hydrogen atoms? Do I need to manually add them? I asked
> this because hydrogen atoms on my oligosaccharide were added automatically
> with loadpdb command, as
> Leap added 57 missing atoms according to residue templates:
> 57 H / lone pairs
> The file contained 3323 atoms not in residue templates
>
> And the total charge is 0 now, which should be +1 according to the protein's
> COO and NH3 sidechains (the sugar is neutral).
>
> Could anyone please help me out?
>
> Thank you.
>
> Yun
>
>
>
> On Fri, Aug 12, 2011 at 11:28 AM, Lachele Foley (Lists)
> <lf.list.gmail.com>wrote:
>
>> Before reordering, I would just insert TER cards between each residue.
>> This will instruct leap not to try bonding them. Then, in leap, you
>> can use the "bond" command to link the residues together properly.
>> Still laborious, but not quite as much.
>>
>> Sorry... no script.
>>
>>
>> On Fri, Aug 12, 2011 at 1:53 PM, Yun Shi <yunshi09.gmail.com> wrote:
>> > Thanks a lot Lachele!
>> >
>> > You are right that the ordering of my molecule is reverse. But changing
>> the
>> > ordering manually seems to be laborious, do you have a script to do this
>> > kind of thing as there are also CONECT records in the pdb file?
>> >
>> > Anyways, I will try changing the order manually first.
>> >
>> > Yun
>> >
>> > On Fri, Aug 12, 2011 at 10:29 AM, Lachele Foley (Lists)
>> > <lf.list.gmail.com>wrote:
>> >
>> >> The ordering of the atoms shouldn't matter. The ordering of the
>> >> residues can make a huge difference.
>> >>
>> >> For example, if you have DGlcpa1-4DManpA1-OH, the three residues are,
>> >> in the order of that string, "0GA", "4MA" and "ROH". However, in the
>> >> pdb file, they need to be ordered ROH first, then 4MA and 0GA.
>> >>
>> >> If the ordering is wrong, you can get around it by inserting TER cards
>> >> between all the residues and setting the bonding explicitly in tleap.
>> >>
>> >> If that still doesn't help, send me your pdb file (you don't have to
>> >> send to the list), and I'll help.
>> >>
>> >> :-) Lachele
>> >>
>> >>
>> >> On Fri, Aug 12, 2011 at 1:19 PM, Yun Shi <yunshi09.gmail.com> wrote:
>> >> > Thank you for the reply.
>> >> >
>> >> > But I want to keep the coordinates as in the original pdb file, and I
>> do
>> >> > notice that the ordering of atoms in my pdb file are different from
>> >> GLYCAM
>> >> > convention.
>> >> >
>> >> > So could anyone suggest a way to format my oligosaccharide in
>> accordance
>> >> > with GLYCAM06 while retaining the coordinates (structure) of my
>> original
>> >> pdb
>> >> > file?
>> >> >
>> >> > Thanks,
>> >> >
>> >> > Yun
>> >> >
>> >> >
>> >> > On Fri, Aug 12, 2011 at 10:00 AM, Oliver Grant <
>> olivercgrant.gmail.com
>> >> >wrote:
>> >> >
>> >> >> Hi,
>> >> >>
>> >> >> Not sure what the problem is without looking at your pdb input file.
>> I
>> >> >> suggest going to glycamweb and building your oligosaccharide and
>> >> comparing
>> >> >> that to what you have.
>> >> >>
>> >> >> Oliver
>> >> >>
>> >> >> On 12 August 2011 04:42, Yun Shi <yunshi09.gmail.com> wrote:
>> >> >>
>> >> >> > Hi All,
>> >> >> >
>> >> >> > Sorry for this lower-level question, but I searched the archive and
>> >> still
>> >> >> > did not solve it.
>> >> >> >
>> >> >> > So I was trying to load a pdb file (only one oligosaccharide
>> molecule)
>> >> >> > after
>> >> >> > source leaprc.GLYCAM_06, but what I got was
>> >> >> >
>> >> >> > ERROR: Comparing atoms
>> >> >> > .R<0hA 1>.A<C3 14>,
>> >> >> > .R<0hA 1>.A<C1 1>,
>> >> >> > .R<0hA 1>.A<H2 19>, and
>> >> >> > .R<0hA 1>.A<O2 20>
>> >> >> > to atoms
>> >> >> > .R<0hA 1>.A<C3 14>,
>> >> >> > .R<2hA 1>.A<C1 1>,
>> >> >> > .R<0hA 1>.A<H2 19>, and
>> >> >> > .R<0hA 1>.A<C1 1>
>> >> >> > This error may be due to faulty Connection atoms.
>> >> >> > !FATAL ERROR----------------------------------------
>> >> >> > !FATAL: In file [chirality.c], line 140
>> >> >> > !FATAL: Message: Atom named C1 from 2hA did not match !
>> >> >> > !
>> >> >> > !ABORTING.
>> >> >> >
>> >> >> > So what it really means by "faulty Connection atoms"? I have
>> already
>> >> >> > changed
>> >> >> > the sugar names according to GLYCAM naming convention.
>> >> >> >
>> >> >> > Any help is appreciated!
>> >> >> >
>> >> >> > Yun
>> >> >> > _______________________________________________
>> >> >> > AMBER mailing list
>> >> >> > AMBER.ambermd.org
>> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >> >
>> >> >> _______________________________________________
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>> >> >>
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>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> :-) Lachele
>> >> Lachele Foley
>> >> CCRC/UGA
>> >> Athens, GA USA
>> >>
>> >> _______________________________________________
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>> >
>>
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> Athens, GA USA
>>
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>>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Aug 12 2011 - 19:30:03 PDT
