Hi JiYuan,
This is normal. You are only at the force constant part of the process. There are more steps to take to generate the charges.
The "X" atom type is fine too. Nothing to worry about - it is an alias for any atom.
Martin
On 21 Nov 2011, at 04:33, JiYuan Liu wrote:
>
> Hi Martin,
> I rename the fchk file and log file of gaussian output,it can
> generate frcmod and prep file now.But I found the new problem,in my prep
> file the charge of every atoms are zero,and in the IMPR line of frcmod it
> presented "X" ,I don't know the "X" represent what.Please take a look in my
> attachment and help me,thank you.
> -------- åå§é®ä»¶ --------
> å件人: Martin Peters <martin.b.peters.me.com>
> åéæ¶é´: 2011-11-19 01:15
> æ¶ä»¶äºº: AMBER Mailing List <amber.ambermd.org>
> 主ãé¢: Re:Re: [AMBER] Can't get the correct gaussian input name after
> runed*_sidechain.bcl in MCPB
> Hi JiYuan,
> This is just a naming issue. I will make the necessary changes to the code
> to ensure it doesn't happen in future releases. Rename and rerun. Let us
> know if you run into more problems.
> Regards,
> Martin
> On 18 Nov 2011, at 07:12, JiYuan Liu wrote:
>>
>> Hi,
>> When I runed *_sidechain.bcl,I can nomally get the gaussian opt file
> named
>> *_sidechain_opt.com and the fc file named *._sidechain_fc.com,I used
>> Gaussian to carry out optimization and frequency calculations,I can get
> the
>> *_sidechain_opt.fchk ,*_sidechain_opt.log and
>> *._sidechain_fc.fchk,*._sidechain_fc.log.But I looked for the
>> *_sidechain_fc_sem.bcl,
>> ----------------*_sidechain_fc_sem.bcl------------
>> ...
>> # Read G03 Formatted Checkpoint file
>> readFormattedChkPtFile NAME_sidechain_opt_md.fchk
>> ...
>> -----------------------------------------------
>> It needs the file named *_sidechain_opt_md.fchk,not
> *_sidechain_opt.fchk,I
>> want to know the file named *_sidechain_opt_md.fchk is corresponded to
>> *_sidechain_opt.fchk?
>> The same question in *_sidechain_fc_md.bcl,
>> ------------------*_sidechain_fc_md.bcl-----------
>> ...
>> # Read G03 file
>> readG03Output 3H68_OH_sidechain_fc_md.log
>> ...
>> -----------------------------------------------
>> *_sidechain_fc_md.log correspond to *_sidechain_fc.log?
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Nov 21 2011 - 01:00:04 PST
