Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW

From: JiYuan Liu <>
Date: Fri, 30 Dec 2011 21:03:09 +0800

Hi Ben,

Thank you very much for these so detailed mailing list etiquette,I have
studied more about it.Please forgive me who is a beginner for maillist,I
will pay more attention in the next time.

Do you think the wrong calib.xml is a crucial reason that related to the
ligand deforming in the minimization?

Have a good vacation:)

于 2011年12月29日 22:58, Ben Roberts 写道:
> Hi JiYuan,
> On 29/12/2011, at 8:22 a.m., JiYuan Liu wrote:
>> Hi,
>> I found a problem with my ligand for it's charge,because my ligand
>> includes dicarboxylic acid,so it' charge could be -2.But when I added my
>> ligand to MCPB,I used the command "antechamber -i ca.pdb -fi pdb -o
>> ca.prepin -fo prepi -c bcc -s 2" and "parmchk -i ca.prepin -f prepi -o
>> ca.frcmod" to get the files ca.frcmod and ca.prepin,I forgot to add "-nc
>> -2" to the first command,then I used frcmod2xml,prep2xml to convert
>> ca.frcmod,ca.prepin,so I got the wrong calib.xml.
>> My question is that if I used this wrong calib.xml in MCPB,could it only
>> affect the partial charges for metal center?The force constants of metal
>> center is affected too?
> I notice that you sent the exact same query to the mailing list on a different thread 36 hours before you sent this copy.
> Please be aware that most Amber experts reside in North America or Europe. Which means that this is our Christmas vacation period. Most of us are travelling or spending time with our families, rather than attending to the Amber mailing list. Also, many of the organisations at which we work are closed. Normal response times will not prevail until early to mid January.
> Furthermore, posting the same query multiple times within a few days is not encouraged at any time of year. If we don't get back to you straight away, it's most likely to mean one of several things: We're having difficulty understanding your question, we understand your question but don't have an answer, or we're too busy with other tasks. Please understand that we are not paid to provide support for the free software packages that make up AmberTools (of which MTK++ is one), and we have other responsibilities that must often take precedence.
> If you think your question has gone unanswered because all the knowledgeable people missed or overlooked it, I suggest you wait at least a week before sending it a second time. If you send it (your question) a second time after a week or more and still don't get an answer, it's likely because no-one knows the answer, and you therefore may as well stop asking for the time being. This does not mean the question will forever go unanswered; but what it does mean is that to find the answer would require a fair amount of detective work and possibly some programming, in which case you're unlikely to have your question resolved for several weeks at least.
> Also, please don't use old threads for new or unrelated topics. If your new question is directly related to the previous thread's subject, then that's OK. But posting a new question on an old or unrelated thread makes following discussions painful. This is especially the case when re-posting previously asked questions: if you must do this, please do so within the thread in which you first asked the question. If you're not continuing an earlier discussion, you're almost always better off starting a new thread (which you do by composing a new message, *not* by "replying" to an old message and editing the subject line).
> Mailing list etiquette aside, and looking at your question:
> My suggestion to you is to run the same sequence of commands on a copy of the input data, but using the correct "-nc" switch. Then compare and contrast the two "calib.xml" files, i.e., the one you already have and the new one that you make. What are the differences? I suspect that the force constants will be unaffected, seeing as they derive from a frequency calculation, but I can't be certain of that.
> Hope that helps,
> Ben
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Jiyuan Liu
Key Laboratory of Plant Protection Resources and Pest Management,National Ministry of Education
Northwest A&F University
Yangling, Shaanxi
China 712100
Phone: 86-29-87092190
AMBER mailing list
Received on Fri Dec 30 2011 - 05:30:03 PST
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