Hi,
If you want to simulate a peptide/protein with an NHE residue in ff02
properly, then you will need to "create" that residue for the ff02
force field. Because it seems like most of the underlying parameters
are already in parm99.dat and frcmod.ff02pol.r1, this should come down
to deriving charges for NHE in a manner consistent with how the rest
of the residues (or more properly, residue fragments) were done.
I would suggest reading the ff02 section of the latest AmberTools
manual (pages 22-23) and reference 22 given therein (Cieplak,
Caldwell, and Kollman, J Comput Chem 2001, 22:1048-1057). This will
give you the background on how the charge derivation was done for this
force field. Then I would suggest looking at the tutorials on the
AMBER website regarding the creation of custom molecules/residues
(e.g., B4 or A1), as well as the antechamber tutorial page (
http://ambermd.org/antechamber/example.html
).
Last, but not least, I think you should consider Prof. Case's advice
in response to your previous question a few days ago: do you really
need/want to use this polarizable force field or would you be just as
well-off using ff99SB or ff03? What advantage(s) does it offer for
your study?
Hope that helps,
Paul
On Jul 14, 2010, at 12:19 AM, llduan.itcs.ecnu.edu.cn wrote:
> Yes, I know in ff02pol there is not NHE residue, but I want to know
> how to
> deal with the NHE residue in ff02pol?
> Thank you
>
>
>
>> Hi,
>>
>> You are getting that error because there is no NHE residue in
>> all_aminoct02.lib, the library file for ff02 C-terminal residues.
>> These files are located in $AMBERHOME/dat/leap/lib if you want to see
>> which residues are available and which are not.
>>
>> Best,
>>
>> Paul
>>
>>
>> On Jul 13, 2010, at 7:49 AM, llduan.itcs.ecnu.edu.cn wrote:
>>
>>>> Dear amber committee
>>>> I am using the ff02 polarizable force field, why I cannot load the
>>>> NHE
>>> residue? My leapin is following
>>>
>>> source leaprc.ff02pol.r1
>>>
>>> set default PBradii mbondi2
>>> pep = sequence {NSER TRP THR TRP GLU ASN GLY LYS TRP THR TRP LYS
>>> NHE }
>>> savepdb pep peptide_linear.pdb
>>> saveamberparmpol pep pep.top pep.crd
>>> quit
>>>
>>>
>>> but the error is :sequence: Illegal UNIT named: NHE
>>>
>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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>>
>
>
>
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Received on Wed Jul 14 2010 - 08:00:04 PDT
