Hi Jinfeng,
Can you provide more information? You can send an separate email to me at ambermailpengfei.gmail.com.
The following sentences are from the tutorial
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm, and it can also be applied to your case.
In order to faciliate the problem-solving procedure, in your email please attach: A. the MCPB.py input file (in the following example is 1OKL.in); B. the referred PDB, mol2, and frcmod files in the MCPB.py input file (in the following example these files are: 1OKL_fixed_H.pdb, ZN.mol2, MNS.mol2, MNS.frcmod); C. the Gaussian calcualted fchk file for the small model (in the following example is 1OKL_small_opt.fchk), and the Gaussian calculated log file for the large model (in the following example is 1OKL_large_mk.log) if you have problems for running step 2 and step 3 of MCPB.py modeling, respectively.
Pengfei
> On Dec 3, 2018, at 6:42 AM, Jinfeng Chen <201612095.mail.sdu.edu.cn> wrote:
>
>
> Hello AMBER users,
> I need to construct a metal contain system, thus I used the MCPB.py bu
> Pengfei Li, but after following the tutorial, I get an error in tleap like
> this :
> ----------------------------------------------------------------------------
> ----------------------------------------------
> /home/hj/program/amber18/bin/teLeap: Error!
> For atom (.R<AL1 380>.A<CL2 1>) could not find vdW (or other) parameters for
> type (Y1)
> /home/hj/program/amber18/bin/teLeap: Error!
> For atom (.R<AL1 380>.A<CL3 2>) could not find vdW (or other) parameters for
> type (Y2)
> /home/hj/program/amber18/bin/teLeap: Error!
> For atom (.R<AL1 380>.A<O4 3>) could not find vdW (or other) parameters for
> type (Y3)
> /home/hj/program/amber18/bin/teLeap: Error!
> For atom (.R<AL1 380>.A<O6 5>) could not find vdW (or other) parameters for
> type (Y4)
> /home/hj/program/amber18/bin/teLeap: Error!
> For atom (.R<AU1 381>.A<AU 1>) could not find vdW (or other) parameters for
> type (M1)
> ----------------------------------------------------------------------------
> ----------------------------------------------
> So whats the problem? And how to solve the problem?
> Any suggestion will be apprecialted.
> Thank you !
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Received on Sat Dec 08 2018 - 19:00:03 PST
