Dear Arturas,
> My system is just a simple peptide that binds into another protein. So,
> I need just one independent modified amino acid to develop. Initial
> conformation I have chosen to minimize with Gaussian was manually
> created to cover essential geometry changes could happen. To be
> precise, the number of ESP points is much less than in A1 (new)
> tutorial - I used Gaussian run based on antechamber creates Gaussian
> input. The number of ESP points is ~8000 and 22 atoms. This
> alpha-carboxyl-glutamic acid has charge -2. I guess this is the source
> of all level, but maybe I'm wrong, because I try first time to go for
> charge derivation for amber FF. I want to stick to standard ff99SB as
> close as possible in charge scheme. One important point - I have used
> resp within AMBER 9 distro.
>
> After many many different tries playing with resp modifying fitting
> procedure, I could not get any reasonable charge on CA. It was the only
> atom which was spoiling all fitting. Also tried to target fitting
> charges to Mulliken from Gaussian output - helped not much. As far as
> amber FF tends to use fitted charges, it shoul be used all residue (not
> like e.g. CHARMM where you can have sero-charge fragments). Something
> worked than I compared my residue to standard GLU and ASP. Along with
> caps, I have frozen NH, CO to GLU and ASP values (they are the same).
> ALSO, I manually put charge -0.05 on CA (something more negative than
> standard GLU/ASP as my reside is -2 e). After playing with restrains I
> managed to get "rational" charge scheme. Using this approach my
> aliphatics hydrogens (CB,...) are positive and carbons negative
> (physically expected, but in opposite to ff99). Maybe amber community
> will not crucify for this approach :)
Let's forget all that.
> Gaussian outputs are attached in tar.gz.
I guess these 3 Gaussian outputs correspond to optimized geometries
because what you sent me are single points. Using the files you sent
me (considered as geometry optimization outputs), I did a basic test
using R.E.D.-IV (this can be done with R.E.D.-III.1 as well) and the
P2N file provided below as a starting point. Here, is what I got using
four molecular orientations for each optimized conformation:
[fyd.master0 R.E.D.IV]$ grep "CA" Mol_MM/*.mol2
Conf._1:
Mol_m1-o1-mm2.mol2: 3 CA -0.787076 -0.247015 0.153977 C 1 UNK 0.2950
Conf._2:
Mol_m2-o1-mm2.mol2: 3 CA -0.761947 -0.217922 0.106399 C 1 UNK 0.1043
Conf._3:
Mol_m3-o1-mm2.mol2: 3 CA 0.575288 0.129971 0.191250 C 1 UNK 0.0932
Conf._1+2+3:
Mol_m4-o1-mm2.mol2: 3 CA -0.787076 -0.247015 0.153977 C 1 UNK 0.2410
Mol_m4-o2-mm2.mol2: 3 CA -0.761947 -0.217922 0.106399 C 1 UNK 0.2410
Mol_m4-o3-mm2.mol2: 3 CA 0.575288 0.129971 0.191250 C 1 UNK 0.2410
(last column: charge values)
The stricking differences between CA charges (conformations 1, 2 & 3:
0.1 up to 0.3!) come from the fact that you have various salt
briges... I also looked at ESP charges; all is fine for me.
I think you should use R.E.D. & follow what is described .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
Tell me what you want me to do... Do you want to send me your whole
job as a single .tar.gz file so that I can look at what goes wrong ?
(in this case rename all the .com files into .com.o because our mail
server rejected all .tgz file with .exe/.com files; protection against
viruses).
> P.S.-1I have checked AMBER mailing list regarding resp - tons of
> messages. I could not find something direct what is the *standard*
> procedure to develop charges for amino acids ?
P. Cieplak, W.D. Cornell, C. Bayly & P.A. Kollman, Application of the
multimolecule and multiconformational RESP methodology to biopolymers:
Charge derivation for DNA, RNA, and proteins. J. Comput. Chem. 1995,
16, 1357-1377
regards, Francois
A typical P2N file to get quick results with R.E.D.-III/IV:
REMARK TITLE beta-carboxylate-glutamic_acid
REMARK CHARGE-VALUE -2
REMARK MULTIPLICITY-VALUE 1
REMARK
REMARK INTRA-MCC 0.0 | 1 2 3 4 5 6 | Remove
REMARK INTRA-MCC 0.0 | 21 22 23 24 25 26 | Remove
REMARK
REMARK REORIENT 7 9 19 | 19 9 7 | 7 9 11 | 11 9 7
REMARK
ATOM 1 H141 UNK 1 3.102 -3.150 0.725 H11
ATOM 2 C14 UNK 1 2.600 -3.011 -0.229 C1
ATOM 3 H142 UNK 1 1.697 -3.612 -0.222 H12
ATOM 4 H143 UNK 1 3.255 -3.331 -1.028 H13
ATOM 5 C2 UNK 1 2.251 -1.541 -0.423 C2
ATOM 6 O3 UNK 1 2.817 -0.873 -1.254 O2
ATOM 7 N4 UNK 1 1.307 -1.103 0.425 N
ATOM 8 H4 UNK 1 0.674 -1.808 0.771 H
ATOM 9 C5 UNK 1 0.575 0.130 0.191 CA
ATOM 10 H5 UNK 1 0.163 0.129 -0.806 HA
ATOM 11 CT6 UNK 1 -0.600 0.216 1.204 CB
ATOM 12 H6 UNK 1 -0.329 -0.367 2.076 HB1
ATOM 13 H6 UNK 1 -0.706 1.245 1.537 HB2
ATOM 14 C7 UNK 1 -1.954 -0.257 0.652 CG
ATOM 15 H7 UNK 1 -2.632 -0.333 1.502 HG
ATOM 16 C8 UNK 1 -1.869 -1.718 0.104 CD1
ATOM 17 O9 UNK 1 -1.110 -2.474 0.765 OG1
ATOM 18 O9 UNK 1 -2.548 -2.026 -0.864 OG2
ATOM 19 C10 UNK 1 1.422 1.386 0.327 C
ATOM 20 O11 UNK 1 2.414 1.499 1.006 O
ATOM 21 N12 UNK 1 0.877 2.417 -0.359 N3
ATOM 22 H12 UNK 1 -0.064 2.270 -0.698 H3
ATOM 23 C13 UNK 1 1.360 3.754 -0.174 C4
ATOM 24 H131 UNK 1 2.422 3.809 -0.384 H41
ATOM 25 H132 UNK 1 0.836 4.411 -0.859 H42
ATOM 26 H133 UNK 1 1.207 4.124 0.840 H43
ATOM 27 C8 UNK 1 -2.585 0.818 -0.277 CD2
ATOM 28 O9 UNK 1 -3.797 0.987 -0.187 OG3
ATOM 29 O9 UNK 1 -1.790 1.481 -0.988 OG4
CONECT 1 2
CONECT 2 1 3 4 5
CONECT 3 2
CONECT 4 2
CONECT 5 1 6 7
CONECT 6 5
CONECT 7 5 8 9
CONECT 8 7
CONECT 9 7 10 11 19
CONECT 10 9
CONECT 11 9 12 13 14
CONECT 12 11
CONECT 13 11
CONECT 14 11 15 16 27
CONECT 15 14
CONECT 16 14 17 18
CONECT 17 16
CONECT 18 16
CONECT 19 9 20 21
CONECT 20 19
CONECT 21 19 22 23
CONECT 22 21
CONECT 23 21 24 25 26
CONECT 24 23
CONECT 25 23
CONECT 26 23
CONECT 27 14 28 29
CONECT 28 27
CONECT 29 27
END
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Received on Fri Jan 30 2009 - 01:39:00 PST
