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 Biocccchimie Théorique e-mail : cailliez.ibpc.fr IBPC 13, rue Pierre et Marie Curie 75005 Paris __________________________________________________________________
>>
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>>
>>
>
>
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Received on Sun Feb 26 2006 - 06:10:16 PST
