Hi:
I have some problems about TIP4P water model.
I can use well with TIP3P water model in my calculation. However, there are
some warnings when I used TIP4P ( please see the following part). Is there
any body would like to help me.
Here is my problem.
My leap.in file is as following:
source leaprc.ff99SB
source leaprc.gaff
WAT=TP4
loadamberparams frcmod.tip4p
MOL=loadmol2 MEA-2.mol2
solvatebox MOL TIP4PBOX 15.0
saveamberparm MOL MEA.prmtop MEA.inpcrd
quit
However, I got some warnings for the last step (saveamberparm MOL MEA.prmtop
MEA.inpcrd) as showed in the following part:
------- .R<WAT 1380>.A<EPW 4> and .R<WAT 1380>.A<O 1>
WARNING: There is a bond of 0.150226 angstroms between:
------- .R<WAT 1381>.A<EPW 4> and .R<WAT 1381>.A<O 1>
WARNING: There is a bond of 0.149723 angstroms between:
------- .R<WAT 1382>.A<EPW 4> and .R<WAT 1382>.A<O 1>
WARNING: There is a bond of 0.149746 angstroms between:
------- .R<WAT 1383>.A<EPW 4> and .R<WAT 1383>.A<O 1>
WARNING: There is a bond of 0.149566 angstroms between:
------- .R<WAT 1384>.A<EPW 4> and .R<WAT 1384>.A<O 1>
WARNING: There is a bond of 0.149405 angstroms between:
------- .R<WAT 1385>.A<EPW 4> and .R<WAT 1385>.A<O 1>
WARNING: There is a bond of 0.149967 angstroms between:
------- .R<WAT 1386>.A<EPW 4> and .R<WAT 1386>.A<O 1>
WARNING: There is a bond of 0.150217 angstroms between:
------- .R<WAT 1387>.A<EPW 4> and .R<WAT 1387>.A<O 1>
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 0 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
MOL 1
)
(no restraints)
I want to know it is normal thing for using TIP4P model becasue I never use
TIP4P model before. Or there is some problems for my leap.in file?
Thank you in advance
--
Best Wishes
Sincerely Yours
Hong-bin Xie
--
Best Wishes
Sincerely Yours
Hong-bin Xie
---------------------------------------------------------------
Hong-bin Xie
Postdoctoral Researcher
Department of Chemical Engineering
University of Pittsburgh
Email:xhbxhb1980224.gmail.com <Email%3Axhbxhb1980224.gmail.com>
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Received on Wed Jul 14 2010 - 10:30:03 PDT
