AMBER Archive (2008)

Subject: Re: AMBER: antechamber and charmm

From: Alan (alanwilter_at_gmail.com)
Date: Thu Jul 17 2008 - 11:05:40 CDT

Thansk for replying Junmei.

So you mean, this fix is not in amberTools 1.1, right? Because I've
digging in charmmgen.c code (from amberTools 1.0) and trying to
understand why period for IMPHI is set to 0 (zero) and not taken from readparm.

More precisely, at line 3469 from charmmgen.c, function wrt_improper():
                                   if (improperparm[j].flag == 0) {
                                               fprintf(ffout, "%2s
%2s %2s %2s%10.3lf%10.0lf%10.1lf\n",
                                                       improperparm[j].name1,
                                                       improperparm[j].name2,
                                                       improperparm[j].name3,
                                                       improperparm[j].name4,
                                                       improperparm[j].force,
                                                       0.0,
<--------------------------------------- Why and not
improperparm[j].fterm ?
                                                       improperparm[j].phase);
                                               improperparm[j].flag = 1;
                                   }

Is that the fix you have you mind?

BTW, would be nice if every new release of amberTools were announced
here in the list, because I didn't see here any mention to AmberTools
1.1.

Cheers,
Alan

On Thu, Jul 17, 2008 at 3:33 PM, Junmei Wang <junmwang_at_gmail.com> wrote:
> Hi, Alan,
> That's bug has been corrected in the next version of ambertools.
>
> Best
>
> Junmei
>
> On Thu, Jul 10, 2008 at 4:43 AM, Alan <alanwilter_at_gmail.com> wrote:
>>
>> Hi List,
>>
>> I used antechamber to generate topologies for charmm. Looking at *.prm
>> I found weird this:
>>
>> c3 ca ca ca 1.100 0 180.0
>>
>> while from gaff.dat, it is:
>>
>> ca-ca-ca-c3 1.1 180. 2.
>>
>> Basically period 2 from gaff is getting 0 in charmm file. It happend
>> to all my impropers. Any special reason for that?
>>
>> Many thanks in advance.
>> Alan
>>
>> --
>> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
>> Department of Biochemistry, University of Cambridge.
>> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>> >>http://www.bio.cam.ac.uk/~awd28<<
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>
> 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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