Dear Lachele
Thanks for your detailedreply, and sorry for my ambiguous question. I think I need make it more clearly.
As I say, I want prepare parameters for protein and a monosaccharide (non-bounded) in a crystal PDB structure, not a sugar alone.
If a sugar alone, we can just do that:
source leaprc.GLYCAM_06j-1
MAN = sequence {ROH 0MA}
saveamberparm MAN MAN.parm7 MAN.rst7
It is OK. But it was not what I want. I find I can 'JUST' divide my monosaccharide into two residues and change their name to ROH and 0MA for each (see my last post), after which I can get my parameter file for my system successfully complex with protein and mannose:
source leaprc.ff14SB
source leaprc.GLYCAM_06j-1
complex = loadpdb complex.pdb
addions ...
solvatebox ...
saveamberparm complex complex.prmtop complex.inpcrd
###################################################################################
So, u can see, there is NO any 'BUILDING' process for sugar, only thing I do is changing residue names for sugar (and reorder atom O1).
Question comes: Such handling is OK and reasonable???( Personally, I think it is OK, I have checked the structure after this)
But, another question comes: why I need BUILD a sugar's parameter file (change residues' name is so easy) and how to let tleap recognize it for my sugar in the PDB file??
I have tried this:
1):source leaprc.GLYCAM_06j-1
2):MAN = sequence {ROH 0MA}
3):saveoff MAN man.lib
then, keep mannose's name in MAN, then load PDB
1):source leaprc.ff14SB
2):source leaprc.GLYCAM_06j-1
3): complex = loadpdb complex.pdb
tleap cannot recognize MAN successfully, I check the .lib file, MAN consist of two residues: ROH and 0MA, my sugar's residue name is MAN, maybe something wrong is here.
I just want to know how to using such BUILDING process to prepare protein with sugar
#####(I am not interested in sugars' alternative conformers, I just want to prepare files to run MD). ######
I can simply change name to let tleap recognize them by GLYCAM force field, but when oligosaccharides get longer, it maybe painful and easy to get errors. Building oligosaccharides on GLYCAM-Web is easy, but, emphasize again, I don't want the parameter file for sugars alone, but complex with protein, and I don't know how to do it with such BUILDing process.
Thank you for your attention!
Chris
At 2015-05-26 09:02:55, "Lachele Foley" <lf.list.gmail.com> wrote:
>I presume you mean "what is the purpose of buliding oligosaccharides
>using GLYCAM-Web?". If you want to know why you need to source a
>GLYCAM parameter set, I can answer that too, but it's a different and
>longer answer.
>
>If you are willing to learn tleap, you don't need the website in most
>cases, but the more complex oligosaccharides can become painful to
>build using tleap, and casual modelers probably don't want to bother
>with tleap at all. In short, the purpose of the site is to simplify
>modeling for people, whether they are seasoned modelers or brand new
>(and intimidated even by a monosaccharide).
>
>But...
>
>There aren't always PDB files for sugars at all. And, when there are,
>the files often represent only one of several (or many) conformers
>present in solution. That is, GLYCAM-Web provides a structures that
>are difficult to obtain experimentally. It can also help you to
>ensure that a monosaccharide in a PDB file is the one it claims to be
>by comparing structures.
>
>Even with a monosaccharide hexose the exocyclic torsions can occupy 2
>or 3 rotamers. Of course, as you might have noticed, the website
>currently doesn't provide multiple rotamers for monosaccharides, but
>it could. No one has yet asked for that. Anyhow...
>
>Did you ever use this command?
>
>saveamberparm MAN MAN.parm7 MAN.rst7
>
>That command is the real test, as it provides the files necessary for
>MD simulations. In amber14, I notice that it renames the ROH residue,
>but still builds as if it is the two residues (this is good). It
>doesn't add ROH hydrogen well, no matter how I try loading your pdb
>file, but a quick minimization will fix that. I didn't try any
>earlier versions of tleap.
>
>
>On Mon, May 25, 2015 at 9:52 AM, Chris <dlutlife223.163.com> wrote:
>> Dear All!
>>
>> Simply put:
>> If I have a a-D-mannose Monosaccharide in my pdb file goes that:
>>
>> HETATM 4532 C1 MAN A1277 44.674 66.009 49.225 0.50 18.65 C
>> HETATM 4533 C2 MAN A1277 44.414 66.755 47.946 0.50 11.67 C
>> HETATM 4534 C3 MAN A1277 42.968 66.536 47.566 0.50 9.58 C
>> HETATM 4535 C4 MAN A1277 42.596 65.084 47.553 0.50 11.02 C
>> HETATM 4536 C5 MAN A1277 42.882 64.500 48.925 0.50 17.80 C
>> HETATM 4538 O1 MAN A1277 44.065 66.677 50.300 0.50 21.39 O
>> HETATM 4537 C6 MAN A1277 42.247 63.221 49.363 0.80 16.97 C
>> HETATM 4539 O2 MAN A1277 45.230 66.211 46.968 0.50 14.32 O
>> HETATM 4540 O3 MAN A1277 42.647 67.158 46.339 0.50 8.06 O
>> HETATM 4541 O4 MAN A1277 41.199 64.988 47.295 0.50 9.50 O
>> HETATM 4542 O5 MAN A1277 44.275 64.669 49.215 0.50 19.81 O
>> HETATM 4543 O6 MAN A1277 43.058 62.461 48.518 0.80 14.19 O
>>
>> I can successfully load this file with tleap after several steps:
>> 1): just change residue name from 'MAN' to '0MA' except atom O1
>> 2): change residue name from 'MAN' to 'ROH' for atom O1
>> 3): mv atom O1 to the top
>>
>> then this file looks like:
>>
>> HETATM 4538 O1 ROH A1277 44.065 66.677 50.300 0.50 21.39 O
>> HETATM 4532 C1 0MA A1277 44.674 66.009 49.225 0.50 18.65 C
>> HETATM 4533 C2 0MA A1277 44.414 66.755 47.946 0.50 11.67 C
>> HETATM 4534 C3 0MA A1277 42.968 66.536 47.566 0.50 9.58 C
>> HETATM 4535 C4 0MA A1277 42.596 65.084 47.553 0.50 11.02 C
>> HETATM 4536 C5 0MA A1277 42.882 64.500 48.925 0.50 17.80 C
>> HETATM 4537 C6 0MA A1277 42.247 63.221 49.363 0.80 16.97 C
>> HETATM 4539 O2 0MA A1277 45.230 66.211 46.968 0.50 14.32 O
>> HETATM 4540 O3 0MA A1277 42.647 67.158 46.339 0.50 8.06 O
>> HETATM 4541 O4 0MA A1277 41.199 64.988 47.295 0.50 9.50 O
>> HETATM 4542 O5 0MA A1277 44.275 64.669 49.215 0.50 19.81 O
>> HETATM 4543 O6 0MA A1277 43.058 62.461 48.518 0.80 14.19 O
>>
>> Then:
>> 4): source leaprc.GLYCAM_06j-1
>> 5): MAN=loadpdb man.pdb
>>
>> All thing goes well with such steps, and tleap successfully generate the parameter file for my pdb.
>> #################################################################################################
>> What I am confused is about the manual:
>>
>> manual said when we make paramers for sugar, we should do something like that:
>>
>> 1): source leaprc.GLYCAM_06j-1
>> 2) MAN = sequence {ROH 0MA}
>> 3)saveoff MAN man.lib or savepdb MAN man.pdb
>>
>> But I don't know how to go next: how can I make tleap recognize my sugar residue in pdb file with method written in manual ??
>> I can simply change the residue names for sugars to make tleap recognize them, so what is the purpose of buliding oligosaccharides using GLYCAM? (If the sugars is not complex)
>>
>> Thx!
>> Appreciate for your reply!
>> Chris
>>
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>--
>:-) Lachele
>Lachele Foley
>CCRC/UGA
>Athens, GA USA
>
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Received on Mon May 25 2015 - 19:30:02 PDT
