[gmx-developers] ffcharmm in gromacs-4.0 patches

[Joshua Adelman]

Hi Erik,

Ok, I'll send it along. I also wanted to note that I followed Justin's  
suggestion of inserting and entry in the ffcharmm.hdb file which  
duplicated the HISA section, renaming it HSD. This seemed to create  
all of the proper outputs from pdb2gmx, as far as I could tell from a  
first look in VMD. I haven't tried to run those files through grompp  
or mdrun yet though.

Josh




On Apr 12, 2009, at 10:41 AM, Erik Lindahl wrote:

> Hi Joshua,
>
> Please send this PDB file to bjelkmar at cbr.su.se (and say that I told  
> you to ;-) - we're working on the final termini patches as well as  
> the histidine detection - including hydrogen-bond-based protonation  
> state selection (I think there could be some hardcoded name changes  
> internally...)
>
> Cheers,
>
> Erik
>
> On Apr 11, 2009, at 8:34 AM, Joshua Adelman wrote:
>
>> I'm attempting to use the ffcharmm force-field found in the cvs  
>> version of gromacs (patches update). I'm having some problems with  
>> pdb2gmx, that I was hoping someone could give me a hand with. I'm a  
>> little new to working with gromacs, so I may be making a really  
>> silly beginner's mistake, but when I run pdb2gmx on my system using  
>> the -ff charmm27 flag (pdb generated by vmd from a namd  
>> simulation), I'm getting a bunch of errors related to the histidine  
>> residues, of the form:
>>
>> WARNING: atom HN is missing in residue HSD 64 in the pdb file
>>        You might need to add atom HN to the hydrogen database of  
>> residue HSD
>>        in the file ff???.hdb (see the manual)
>>
>> The ffcharmm27.hdb does not contain an entry for histidines named  
>> HSD, but does use what looks like the standard gromacs HISA, HISB,  
>> etc. However if you look in the .rtp file, there is an entry for  
>> HSD, HSE but nothing for HISA,HISA, etc. When I look in other  
>> forcefields in the /top directory, it seems like other force fields  
>> are consistent in their naming schemes between these file types  
>> (for example in ffoplsaa.*)
>>
>> I've tried renaming my histidine residues to HIS, using the  
>> interactive -his flag, etc, and I just get different conflicts that  
>> seem to be related to this inconsistency between the files that I  
>> mention above.
>>
>> Is this a problem with the ffcharmm files, or am I just doing  
>> something wrong?
>>
>> Any suggestions would be most appreciated.
>>
>> Josh
>>
>>
>>
>> ------------------------------------------------------------------------------------------------------
>> Joshua L. Adelman
>> Biophysics Graduate Group              Lab: 510.643.2159
>> 218 Wellman Hall                                Fax: 510.642.7428
>> University of California, Berkeley     http://nature.berkeley.edu/~jadelman
>> Berkeley, CA 94720 USA                   jadelman at berkeley.edu
>> ------------------------------------------------------------------------------------------------------
>>
>>
>>
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------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group              Lab: 510.643.2159
218 Wellman Hall                                Fax: 510.642.7428
University of California, Berkeley     http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA                   jadelman at berkeley.edu
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