AMBER Archive (2009)

Subject: Re: [AMBER] How to prepare the acetate ion file in leap?

From: Balazs Jojart (jojartb_at_gmail.com)
Date: Tue Oct 13 2009 - 02:36:03 CDT

Hi,
your pdb doesn't include the hydrogen atoms. Antechamber is not able to
add them, try VMD and the molfacture plugin.
Hope this helps,
Balazs

xuemeiwang1103 wrote:
> Hi:
> I'm going to run a simple MD about a protein system which include a acetate ion.It seems that the leap can't recognize the acetate ion.In order to solve this ,I use the Antechamber command to create the pre files,but the error hapeens ,could somebody help me regarding this or tell me other method to solve the leap problem?
> By the way my acetate ion pdb was extracted from the protein pdb file without modified. Thanking in advance!
>
> acetate pdb:
> HETATM 4746 C ACT A 700 42.190 36.698 47.868 1.00 17.87 C
> HETATM 4747 O ACT A 700 43.358 36.429 48.383 1.00 17.41 O
> HETATM 4748 OXT ACT A 700 41.942 37.484 46.891 1.00 16.00 O
> HETATM 4749 CH3 ACT A 700 41.037 35.966 48.550 1.00 16.17 C
> TER
> END
> ~
> ~
> the error:
> Running: /usr/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase MAXVASTATE in define.h and recompile bondtype.C
> (4) increase PSCUTOFF in define.h and recompile bondtype.C
> Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer time
> Error: cannot run "/usr/local/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit
>
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