AMBER Archive (2006)

Subject: Re: AMBER: AMBER force field with namd

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Feb 23 2006 - 08:04:51 CST

Hi Carlos,

 You are right as far as I remember but I also recall that the point is
clearly stated in the NAMD documentation (hope I am not wrong).

vlad

Carlos Simmerling wrote:

> When using NAMD, make sure to set the correct 1-4 scaling factors!
> I have been told that NAMD does not have the correct default for Amber
> force fields.
>
> Vlad Cojocaru wrote:
>
>> Dear Fabien,
>>
>> Maybe it would be best to post this on the NAMD list .... People could
>> help you more I believe ...
>>
>> First of all, as far as I am aware new versions of NAMD do not require
>> any change of the amber topology for the waters ... Its bin quite a
>> while since I used NAMD and I remember that I had to change the water
>> box ... but as far as I understood the newest versions of NAMD do treat
>> the 3-bonded waters properly ... You should though check with namd
>> people to be sure ... Or run a short simultation with a topology having
>> 3-bonded waters.. If you monitor the angle H-O-H during the simulation
>> and it shrinks ...than you should change the topology but if it stays
>> constant you dont have to change the topology...
>>
>> As for the impropers, as far as I remember this was a harmless message
>> but I do not remember exactly why (I would have to dig into my notebooks
>> for that)... maybe its because NAMD treats the impropers as normal
>> dihedrals ... (please take this as a guess rather than a fact .... maybe
>> check the number of dihedrals ) ...
>>
>> As for the exclusions, I cannot help you with that ... sorry ...
>>
>> vlad
>>
>>
>>
>> Fabien Cailliez wrote:
>>
>>
>>
>>> Dear AMBER users,
>>>
>>> I am trying to use AMBER force field with NAMD. The first problem is
>>> about defining TIP3P waters with no H-H bond and with HOH angle. So
>>> I changed leap according to what is told in the AMBER list (and also
>>> the solvents.cmd to remove H-H bond) and the topology file thus
>>> created seems OK. However, when I load it with NAMD, I see two weird
>>> things : - the number of improper torsions read by NAMD is 0 whereas
>>> leap tells me that the number of improper torsions added is 553. -
>>> thenumber of exclusions read by NAMD (26289) does not match with the
>>> number of exclusion terms in my topology file (30243). I put both
>>> the output of NAMD and the beginning of my topology file at the end
>>> of the mail. Did someone ever noticed that or did I compare the
>>> wrong numbers ?
>>>
>>> When this problem is fixed, I would like to compare AMBER results
>>> with NAMD results from the same starting point to check that
>>> everything is OK. But there is another problem then : I cannot load
>>> the modified topology file into sander because it tells me : Error:
>>> A residue defined as a "fast 3-point water" is not defined by a
>>> triangle of three bonds. Residue 357 contains 2 bonds.
>>>
>>> Thanks in advance for your help and suggestions,
>>> Fabien
>>>
>>> ******************************************* NAMD output :
>>>
>>> Info: SUMMARY OF PARAMETERS: Info: 1342 BONDS Info: 76 ANGLES Info:
>>> 35 DIHEDRAL Info: 0 IMPROPER Info: 0 VDW Info: 153 VDW_PAIRS Info:
>>> **************************** Info: STRUCTURE SUMMARY: Info: 13890
>>> ATOMS Info: 11410 BONDS Info: 8777 ANGLES Info: 9427 DIHEDRALS Info:
>>> 0 IMPROPERS Info: 26289 EXCLUSIONS Info: 41667 DEGREES OF FREEDOM
>>> Info: 5206 HYDROGEN GROUPS Info: TOTAL MASS = 104743 amu Info: TOTAL
>>> CHARGE = -7 e Info: *****************************
>>>
>>> ************************************************ Topology file :
>>> %VERSION VERSION_STAMP = V0001.000 DATE = mm/dd/yy hh:mm:ss %FLAG
>>> TITLE %FORMAT(20a4)
>>>
>>> %FLAG POINTERS %FORMAT(10I8) 13890 17 8684 2726
>>> 6853 1924 5985 3442 0 0
>>> 30243 3997 2726 1924 3442 1342 76 35
>>> 28 1
>>> 0 0 0 0 0 0 0 0
>>> 24 1
>>> 0 0
>>>
>>> --
>>> __________________________________________________________________
>>> Fabien Cailliez Tel : 01 58 41 51 63 Laboratoire de Bioccchimie
>>> Théorique e-mail : cailliez_at_ibpc.fr IBPC 13, rue Pierre et Marie
>>> Curie 75005 Paris
>>> __________________________________________________________________
>>>
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>>>
>>>
>>>
>>
>>
>>
>
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-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/

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