Thank you case!
You are correct. For original mol2, all of these atom types are lower case
and yesterday I change them to upper case mistakenly to make it suitable
with ff99SB. Sorry about that!
Here is the situation now:
The attachments are the pdb file I am trying to load and mol2 file. I can
load mol2 file. When loading pdb file, there will be the following message:
> test=loadpdb 1X6W-H-ok-con.pdb
Loading PDB file: ./1X6W-H-ok-con.pdb
One sided connection. Residue: missing connect1 atom.
One sided connection. Residue: missing connect1 atom.
total atoms in file: 300
Leap added 182 missing atoms according to residue templates:
182 H / lone pairs
for saveamberparm instruction:
> saveamberparm test newff.pcmtop newff.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -14.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: c3 - c3 - o
Could not find angle parameter: cf - ce - ca
Could not find angle parameter: ce - cf - ca
Could not find angle parameter: c3 - c3 - o
Could not find angle parameter: cf - ce - ca
Could not find angle parameter: ce - cf - ca
Building proper torsion parameters.
** No torsion terms for ca-ca-cf-ha
** No torsion terms for ca-ca-cf-ha
** No torsion terms for ca-ca-ce-ha
** No torsion terms for ca-ca-ce-ha
** No torsion terms for cf-ce-ca-ca
** No torsion terms for cf-ce-ca-ca
** No torsion terms for ce-cf-ca-ca
** No torsion terms for ce-cf-ca-ca
** No torsion terms for ca-ca-cf-ha
** No torsion terms for ca-ca-cf-ha
** No torsion terms for ca-ca-ce-ha
** No torsion terms for ca-ca-ce-ha
** No torsion terms for cf-ce-ca-ca
** No torsion terms for cf-ce-ca-ca
** No torsion terms for ce-cf-ca-ca
** No torsion terms for ce-cf-ca-ca
Building improper torsion parameters.
total 86 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
How can I solve that?
Thank you very much!
2009/9/5 Yikan Chen <yc2r.virginia.edu>
> Maybe you sent the wrong mail?...
> I will restate my problem:
> I have a big molecule that is composed with a short DNA duplex and two
> short residues called TMS attaching on the both terminal of duplex. To make
> this molecule recoginzed by Amber, I plan to convert a standard pdb file for
> TMS to a mol2 file by antechamber, and load this mol2 file before I load the
> pdb file of the big molecule. Will this method work? What kind of force
> field should I choose? I am suggested to use GAFF for TMS and ff99SB for the
> big molecule. I have no idea about how to do that.....
> Thanks for any help!
>
> On Fri, Sep 4, 2009 at 2:33 PM, Rilei Yu <yulaomao1983.yahoo.com.cn>wrote:
>
>> Dear Prof. David,
>>
>> This afternoon, I talked too much to you. I know you are really very busy,
>> next time I will discuss my problem in a more appropriated way. For example
>> in the meeting and our discussion time. I think that will be enough. Thanks
>> for your recommendation to the lecturer this afternoon.
>>
>> PhD road is not so smooth, I know, there are also far way for me to go.
>> So every hour I have to prepare to face the challenge in my experiment.
>>
>> Thanks for your help!
>>
>> Having a good weekend.
>>
>> Rilei Yu
>>
>> --- 09Äê9ÔÂ4ÈÕ£¬ÖÜÎå, Yikan Chen <yc2r.virginia.edu> дµÀ£º
>>
>> ·¢¼þÈË: Yikan Chen <yc2r.virginia.edu>
>> Ö÷Ìâ: [AMBER] Problem about adding a small residue to DNA
>> ÊÕ¼þÈË: "AMBER Mailing List" <amber.ambermd.org>
>> ÈÕÆÚ: 2009Äê9ÔÂ4ÈÕ,ÖÜÎå,ÏÂÎç12:33
>>
>> Hi Amber users,
>> The substance I am working on is a small residue called TMS combing with
>> an DNA duplex. In order to make the TMS part recognized by Amber, I also
>> download a pdb file for TMS, and do the following things:
>> antechamber -i TMS_model.pdb -fi pdb -o TMS_model.mol2 -fo mol2 -c bcc -nc
>> -1
>> parmchk -i TMS_model.mol2 -f mol2 -o frmod
>> Everything is fine for these instructions.
>> However, it does not work quite well for loadpdb instruction(in ff99SB).
>> There will be error message:
>> * test=loadpdb 1X6W-H-ok-con.pdb *
>> * Loading PDB file: ./1X6W-H-ok-con.pdb *
>> * One sided connection. Residue: missing connect1 atom. *
>> * One sided connection. Residue: missing connect1 atom. *
>> * total atoms in file: 300 Leap added 182 missing atoms according to
>> residue templates: 182 H / lone pairs*
>> And cannot saveamberparm:
>> * WARNING: The unperturbed charge of the unit: -14.000000 is not zero. *
>> * -- ignoring the warning. Building topology. Building atom parameters. *
>> * For atom: .R<TMS 1>.A<C1 1> Could not find type: CE *
>> * For atom: .R<TMS 1>.A<C20 3> Could not find type: C3 *
>> * For atom: .R<TMS 1>.A<C21 5> *
>> ...
>> What is the meaning of these?
>> Also what is more important is I am puzzled about how to choose force
>> field. It is said I should use gaff for TMS residue and ff99SB for this
>> molecule. How can I do that? Does antechamber work for this situation?
>> Attachment:
>> 1X6W.pdb: the molecule I am working on
>>
>> Thanks!
>> Best,
>> Yikan
>>
>> -----ÏÂÃæΪ¸½¼þÄÚÈÝ-----
>>
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>>
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>>
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>
>
Received on Mon Sep 14 2009 - 11:52:54 PDT
