Dear Carmona
Thanks a lot for your response!
I've already used the command you mentioned to load frcmod file but
returned error messege like below:
--------- error messege ----------
Modified force field files must contain both a MASS and NONB entry, or
neither
Could not load parameter set.
--------------------------------------
I deleted NONB part of this frcmod file( I'm not sure about the
correctness) and hence loaded it without any errors. But I still
couldn't load a pdb in xleap successfully. In additoin, the file
all_rc.tpg is still unkown to me and I'm eager to know what it is.
Any suggestion would be appreciated again. Thanks in advance!
scopio
Juan Fernandez-Carmona wrote:
>scopio a écrit :
>
>
>>Dear AmberUsers:
>>
>>I have a pdb contains some residue that could not be recognized by xleap
>>due to lacking of amber parameters. Fortunately, I get these parameters
>>from a very kind person. But I don't know how to use them. Could anybody
>>check them attached and give me some suggestions? Thanks in advance!
>>
>>By the way, is the mail reflector would filter email larger than 1MB?
>>
>>Regards!
>>
>>scopio
>>
>> --------------------all_rc.prm----------------------------------------------------
>>#
>>#
>># quinone7.prm
>># cromofo_last.prm
>>#
>>#
>>BOND
>>#fe+mg ( k from CHARMM; dist from X-ray)
>>nb fe 65.00 2.10
>>o2 fe 65.00 2.25
>>nb mgc 65.00 2.25
>>........................( igored )
>>END
>>BENDINGS
>>#fe+mg
>>cr nb mgc 0.00 0.00
>>nb mgc nmh 0.00 0.00
>>nb mgc ns 0.00 0.00
>>....................... ( igored )
>>END
>>TORSION PROPER
>>#fe
>>x fe nb x 0.00 4
>>x fe o2 x 0.00 4
>>....................... ( igored )
>>END
>>TORSION IMPROPER
>>x ccs ns mgc 1.100 2.0 180.0 cosine
>>x x nmh mgc 1.100 2.0 180.0 cosine
>>...................... ( igored )
>>END
>>NONBONDED MIXRULE
>>#fe
>>fe 0.740 0.250 0.740 0.250 55.847
>>#my
>>mgc 0.650 0.250 0.000 0.000 24.305
>>nh 1.824 0.170 0.000 0.000 14.010
>>ns 1.824 0.170 0.000 0.000 14.010
>>...................... ( igored )
>>END
>>
>> -------------------all_rc.tpg-----------------------------------------------------
>>RESIDUE bcl ( Total Charge = 0.0 )
>>atoms
>>group
>>mg mgc 0.1340
>>group
>>cha csb 0.0650
>>group
>>chb cab -0.2240
>>hb ha0 0.1150
>>group
>>chc cab -0.2730
>>hc ha0 0.1680
>>............. ( igored )
>>end
>>
>>bonds
>>nb mg nc mg nd mg na mg
>>nb c1b c1b c2b c2b c3b c3b c4b
>>c4b nb
>>nc c1c c1c c2c c2c c3c c3c c4c
>>c4c nc
>>nd c1d c1d c2d c2d c3d c3d c4d
>>c4d nd
>>na c1a c1a c2a c2a c3a c3a c4a
>>c4a na
>>................ ( igored )
>>imphd
>>#
>>c1b c4b nb mg
>>c2b nb c1b chb
>>c1b c3b c2b cmb
>>c4b c2b c3b cab
>>c3b nb c4b chc
>>................ ( igored )
>>end
>>
>>termatom * *
>>RESIDUE_END
>>
>>
>
>you've got to save the parameters in a filename.pcy then in xleap do
>:loadamberparams filename.pcy
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Mar 17 2004 - 09:53:00 PST
